Here are the mdp parameters:
title = POPC cpp = /usr/bin/cpp integrator = md tinit = 0.0 dt = 0.030 nsteps = 3000000 nstcomm = 1 comm-grps = Lipid W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 30000 nstvout = 30000 nstfout = 0 nstlog = 30000 nstenergy = 30000 ns_type = grid nstlist = 10 pbc = xyz rlist = 1.2 ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No ; Temperature coupling = tcoupl = Berendsen tc-grps = Lipid W tau_t = 0.3 0.3 ref_t = 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 3.0 30 compressibility = 3e-5 3e-5 ref_p = 1.0 1.0 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess <[email protected]> wrote: > Hi, > > I am 99.99% sure that there is no problem with COM motion removal in > Gromacs. > Could you post your mdp parameters? > > Berk > > > From: [email protected] > > To: [email protected] > > Subject: Re: [gmx-users] Martini simulation problem in recentering > trajectory so that the bilayer is at the center > > Date: Wed, 2 Sep 2009 16:04:39 +0200 > > > > > > > I am not sure how to fix the trajectory that has drifted ... > > > > But if your bilayer drifts even if you use a removal of the COM for > > the water and > > bilayer separately that means there is problem in the code! And this > > should be > > fixed. > > > > XAvier. > > > > On Sep 2, 2009, at 3:36 PM, maria goranovic wrote: > > > > > Dear Experts > > > > > > I had posted this earlier, but the problem was not solved by earlier > > > suggestions. So am posting again. > > > > > > I am simulating a POPC bilayer using MARTINI. The simulation ran > > > fine, but the bilayer drifted towards the edge of the box along the > > > bilayer normal, and eventually some of the atoms crossed the box > > > boundaries. In some cases, entire lipid molecules crossed the box > > > boundaries. I tried to recenter the trajectory, so that the lipid > > > bilayer would be at the center of the box at all times. But for some > > > reason, this does not seem to work? I have tried simulations using a > > > single comm_group for the entire system, as well as separate ones > > > for the lipid and water, but the same problem appears in either case. > > > > > > Typically, for all-atom bilayers, the following set of commands > > > works to correct the drift: > > > > > > #### first convert original trajectory to a temp. xtc ### > > > echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center - > > > boxcenter zero -pbc mol -n popc.ndx > > > #### then convert temp.xtc to the final trajecory ### > > > echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center - > > > boxcenter zero -pbc mol -n popc.ndx > > > > > > where groups 3 and 0 are the lipid and the whole system > > > respectively, and final.xtc is my final trajectory. > > > > > > However, this does not work for the MARTINI systems. Looking at the > > > final trajectory in VMD, the bilayer is either at the center of the > > > box, or it is split at the box edges, with each monomer being in > > > different leaflets. > > > > > > If I plot the center of mass motion of the entire system in the > > > original trajectory .. the system seems to drift by ~ 2-3 angstroms > > > in one direction. As a result, water center of mass drifts in the > > > opposite direction (because of PBC). > > > > > > Are there any suggestions to sort this out? One option is to write > > > the entire trajectory to .gro files, recenter all of them (depending > > > upon whether the bilayer is in the center or is split at the box > > > edge), and concatenate the gro files again.but this is tedious, even > > > if scripted. > > > > > > Please let me know if i can provide any additional info ? > > > > > > -- > > > Maria G. > > > Technical University of Denmark > > > Copenhagen > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [email protected]. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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