Simulacin en vacio https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/simulations_1.html Force field http://www.mail-archive.com/gmx-users@gromacs.org/msg18028.

html

OPLS has been parametrized on the properties of pure liquids of small > compounds. > For Gromos at least the liquid properties of alkanes have been > checked. > So both force fields would work well for real vacuum simulations.
http://gromacs.5086.n6.nabble.com/Force-Field-for-Vacuum-simulation-td4458797.html
In accordance to the Justin's tutorial I've found that GROMOS96 43b1 force field might be good choice for that task.

comparison of FF for vacuum simulations: Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) Error no Ewald with pbc=no

pbc: no Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs to 0 and nstlist=0. For best performance without cut-offs, use nstlist=0, ns_type=simple and particle decomposition instead of domain decomposition.
http://comments.gmane.org/gmane.science.biology.gromacs.user/41605

Feb 06, 2004; 8:14am Vacuum simulations

md.mdp title = Rec-Lig MD cpp = /lib/cpp define = POSRE_TM constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 2000000 ; total 2 ns. ;nstcomm = 1 nstxout = 50000 nstvout = 50000 nstfout = 50000 nstlog = 50000 nstenergy = 50000 nstxtcout = 50000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 4 vdwtype = cut-off rvdw = 1.4 pbc = no comm_mode = linear nstcomm = 1 comm_grps = system ; protein_drg ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein drg ref_t = 300 300 ; Energy monitoring energygrps = system ; protein_drg ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 031775

sa.mdp title = Rec-Lig SA cpp = /lib/cpp define = POSRE_TM constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 1000000 ; total 1 ns. ;nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb = 1.4 epsilon_r = 4 vdwtype = cut-off rvdw = 1.4 pbc = no comm_mode = linear nstcomm = 1 comm_grps = protein_drg ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein drg ref_t = 600 600 ; Energy monitoring energygrps = protein drg ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 ; Simulated annealing annealing = yes zero_temp_time = 1000 ; ps ; Generate velocites is on at 900 K.

gen_vel gen_temp gen_seed

= yes = 600.0 = 031775

Yinghong Jan 28, 2005; 10:17am Simulation in Vacuum em.mdp: //////////////////////// cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 nsteps = 500 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.2 Tcoupl = no Pcoupl = no gen_vel = no //////////////////////////////// pr.mdp: title cpp define constraints integrator dt nsteps nstcomm nstxout = Yo = /lib/cpp = -DPOSRES = all-bonds = md = 0.002 = 5000 = 1 = 50

nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = protein tau_t = 0.1 ref_t = 300 energygrps = system; ;Pressure coupling is off Pcoupl = no ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 /////////////////////////////////////// full.mdp: title cpp constraints integrator dt nsteps nstcomm nstxout nstvout nstfout nstlog nstenergy nstlist = Yo = /lib/cpp = all-bonds = md = 0.002 = 200000 = 1 = 1000 = 10000 = 1000 = 1000 = 1000 = 10

ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = system ; Isotropic pressure coupling is now on Pcoupl = no ; Generate velocites is off at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thomas Schlesier Sep 17, 2008; 9:14am simulation in vacuum

turn off cut off

Set them to zero. And also nstlist = 0. Simulacin en vacio pdb2gmx -f peptide.pdb -o peptide.pdb -v -ignh -ter

where you should choose again the G53a6 force field (option 4) and the option 1 for both terminals. Thus, you will use uncharged amino and carboxylic termini. This is because the electrostatic interactions in vacuum are strong due to its low permitivity and, using charged termini, these groups would tend to stay together throughout the trajectory. To minimize the structure, use the following "em.mdp": title = PEPTIDE ENERGY MINIMIZATION integrator = steep nsteps = 500

nstlist = 1 ns-type = Grid pbc = xyz rlist = 0.8 coulombtype = cut-off rcoulomb = 1.4 vdw-type = cut-off rvdw = 1.4 nstenergy = 20
Gerrit Groenhof (RUG) Aug 09, 2006; 2:23am Re: Vacuum simulation p Do not use Pressure coupling in vacuo. ALso you seem to be running with periodic boundary conditions. Switch that off as well and use ns_type = simple, and finally use infinite cut-offs when simulating in vacuo. qa cut-off of 0.9 is way too short. If you think the lack of water causes the conformatational changes and you don't want that, you can try putting position restraints on backboneatoms of solvent exposed residues. title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 10000000 ; total 10000 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on

Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp = 300.0 gen_seed = 173529

Qinghua Liao Apr 12, 2012; 12:23pm simulations in vacuum in parallel title = PDXN of Abeta in H2O ;cpp = /lib/cpp ; prepocessor of the current machine define = ;-DPOSRES integrator = md ; molecular dynamics algorithm tinit = 0.0 ; start time and timestep in ps dt = 0.002 ; time step in ps nsteps = 500000000 ; number of steps for 1000ns run emtol = 100 ; convergence criterion emstep = 0.05 ; intial step size nstlist = 10 ; step frequency for updating neighbour list ns_type = grid ;simple ; method for neighbour searching (?) nstxout = 5000 ; frequency for writing coords to output .trr file nstvout = 0 ; frequency for writing velocities to output...should be same as nstxout nstfout = 0 ; frequency for writing forces to output nstlog = 5000 ; frequency for writing energies to log file nstenergy = 5000 ; frequency for writing energies to energy file nstxtcout = 5000 ; frequency for writing coords to xtc traj xtc_grps = system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 0 ; cutoff lengths (nm) epsilon_r = 1.0 ; Dielectric constant (DC) for twin-range or DC of reaction field niter = 100 ; Some thingies for future use fourierspacing = 0.16 fourier_nx = 30 fourier_ny = 30 fourier_nz = 30 coulombtype = Cut-off ; truncation for minimisation, with large cutoff rcoulomb = 0 rcoulomb-switch = 0 vdw-type = Cut-off ; truncation for minimisation, with large cutoff rvdw-switch =0 rvdw = 0 ; cut-off lengths ;pme_order = 6 ; EWALD/PME/PPPM parameters

;ewald_rtol = 1e-05 ;ewald_geometry = 3d epsilon_surface =0 optimize_fft = yes Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda =0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 comm_mode = angular nstcomm = 10 ; number of steps for centre of mass motion removal (in vacuo only!) Tcoupl = V-rescale tc_grps = system ; MVN_Protein ;SOL_Ion ; Non-Protein tau_t = 0.01 ref_t = 300 Pcoupl = no ; Parrinello-Rahman ; Pressure coupling ;Pcoupltype = Isotropic ;tau_p = 1.0 1.0 1.0 ;ref_p = 1.0 1.0 1.0 ;compressibility = 4.5e-5 ; compressibility ; annealing = no ; SIMULATED ANNEALING CONTROL ;zero_temp_time = 0 ; Time at which temperature should be zero (ps) gen_vel = yes gen_temp = 300 gen_seed = -1 constraints = all-bonds ; OPTIONS FOR BOND CONSTRAINTS constraint-algorithm = Lincs ; Type of constraint algorithm lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix lincs_iter = 1 lincs_warnangle = 30 ; Lincs will write a warning to the stderr if in one step a bond rotates ; over more degrees than unconstrained-start = no ; Do not constrain the start configuration ;Shake-SOR = no ; Use successive overrelaxation to reduce the number of shake iterations ;shake-tol = 1e-04 ; Relative tolerance of shake morse = no ; Convert harmonic bonds to morse potentials David van der Spoel Jan 12, 2005; 4:51am Re: simulation of the protein in vacuum set all cutoffs to zero, nstlist = 0 and use comm-mode = angular

sapna sarupria Jul 15, 2008; 8:16am Using user-tables for simulations in vacuum Hello users, I am trying to do a simulation of a polymer chain (which is simply a bead of unified methane molecules) in vacuum using user-defined tables. The interactions are WeeksChandler-Andersen instead of Lennard-Jones. However, when I run the simulations, mdrun gives me a segmentation fault. When I run simulations for the exact same configurations without the tables (and therefore using VdW) the simulations run fine. In addition, the starting configurations were obtained after 3ns simulations of the polymer in water. So I was wondering if there is any issue with using user-defined tables with simulations in vacuum. If not do you have any idea what could be going wrong. Some details of the mdp file: 1. pbc is turned off. 2. there is no pressure coupling. 3. center of mass removal is set to angular. 4. temperature is 298 K and berendsen thermostat is used. 5. energy groups and table are defined (correctly). 6. the cut-offs are set to 1.0nm (box size is larger than 4 nm). 7. no constraints are being used.

Joanne Hanna Apr 27, 2005; 1:23pm Enzyme Simulation vacuum, No ligands, Non periodic system Hi I have been trying to grompp my files to run a MD simulation on an enzyme in vacuum without ligands. I have choosen the vacuum force field and have succesfully minimised the enzyme but cannot progress as i get many errors from grompp regarding cut-offs, relating to the values of nstcomm etc. I have fixed a number of these errors by setting the ns_type to simple and also setting all of my cut offs to 0 although i am still using the coulombtype = cut-off option, which i'm not sure is the correct thing to do I cannot however get around this error: WARNING 1 [file md1.mdp, line unknown]: mdrun will apply removal of angular momentum when nstcomm < 0 ..........

.......... There was 1 warning I have attached my *.mdp file below and am requesting any advice as to which options i should be choosing in the *.mdp file as i am now choosing options on a trial and error basis to try and minimise the errors! Many thanks Jo ##### md1.mdp ###### title cpp define integrator tinit dt nsteps nstcomm comm-grps nstxout nstvout nstfout nstlog nstenergy nstxtcout xtc-precision energygrps = Enz No Ligands = /lib/cpp = -DPOSRES = md =0 = 0.001 = 50000 = -1 = = 100 = 500 =0 = 10 = 10 = 100 = 100 = PROTEIN

nstlist = 10 ns-type = simple pbc = no rlist = 0.0 domain-decomposition = no coulombtype rcoulomb-switch rcoulomb epsilon-r = Cut-off =0 = 0.0 =1

; Van der Waals = vdw-type = Cut-off rvdw-switch =0 rvdw = 0.0 DispCorr fourierspacing = No = 0.12

fourier_nx fourier_ny fourier_nz

=0 =0 =0

tcoupl = berendsen tc-grps = PROTEIN tau-t = 0.5 ref-t =0 Pcoupl = no annealing = no ;zero-temp_time =0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen-vel = yes gen-temp = 310 gen-seed = 173529 constraints = all-bonds constraint-algorithm = Shake unconstrained-start = yes shake-tol = 0.00001 lincs-order =4 step a bond = lincs-warnangle = 30 morse = no disre = No Equal or Conservative = disre-weighting = Equal disre-mixed = no disre-fc = 1000 disre-tau =0 nstdisreout = 100 free-energy init-lambda delta-lambda sc-alpha sc-sigma acc-grps accelerate freezegrps freezedim cos-acceleration E-x E-xt E-y E-yt E-z E-zt = = = = = = = no =0 =0 =0 = 0.3 = = = = =0

Respuesta
David van der Spoel This is a warning, not an error. And this is what you want in vacuum. Your current setup will simulate computing all interactions, no cutoff. Which means you can also turn off temperature coupling.

Zoe Hall Jan 11, 2011; 10:29am Simulations in vacuo I am trying to set up a simulation of a large protein in vacuo using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933). Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever.

I am not sure, however, what is the appropriate choice for coulombtype and other electrostatic parameters for vacuum simulations. I have set epsilon_r to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it.

Respuesta
Mark Abraham vdwtype = cut-off coulombtype = cut-off and all the distance cut-offs to zero (which is treated as an infinite cut-off) Erik Marklund I should point out that there is probably an error in the methods section. If I recall correctly we used a 0.5 fs timestep. We couldn't get good conservation of total energy with 1 fs steps. Remember to use double precision, or you will again loose conservation of total erergy. Remember to monitor the total energy, because if it's drifting you need to have a more conservative setup, e.g., use a smaller timestep.

Take a look at our "follow up" study (Marklund et. al., PCCP (2009) 11 p. 8069 8078) where we used LINCS and managed to conserve the total energy with a 1 fs time step. Literatura Vacuo Find other literature. That document is a master thesis and not peer-reviewed material. I know the supervisor, and also the student to some extent, but even if I'd vouch for the methods used you should base your protocol primarily on peer-reviewed publications. In my former group we published a few papers on protein simulations in vacuo (which were all NVE). See e.g. Patriksson et al, Biochemistry 46:933-945 (2007) Wang et al, Biochemistry 48:1006-1015 (2009) Friemann et al, J. Am. Chem. Soc. 131:16606-+ (2009) Marklund et al, PCCP 11:8069-8078 (2009) Van der Spoel et al, Macromol. Biosci. 11:50-59 (2011) Also have a look at the work of Modesto Orozco.