Here are the mdp parameters:<br><br><br>title = POPC<br>cpp = /usr/bin/cpp<br>integrator = md<br>tinit = 0.0<br>dt = 0.030<br>
nsteps = 3000000<br>nstcomm = 1<br>comm-grps = Lipid W<br><br>; OUTPUT CONTROL OPTIONS = <br>; Output frequency for coords (x), velocities (v) and forces (f) = <br>nstxout = 30000<br>
nstvout = 30000<br>nstfout = 0<br>nstlog = 30000<br>nstenergy = 30000<br><br>ns_type = grid<br>nstlist = 10<br>pbc = xyz<br>
rlist = 1.2<br><br>; Method for doing electrostatics = <br>coulombtype = Shift <br>rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift <br>
; cut-off lengths = <br>rvdw_switch = 0.9<br>rvdw = 1.2<br>DispCorr = No<br><br>; Temperature coupling = <br>tcoupl = Berendsen<br>tc-grps = Lipid W<br>
tau_t = 0.3 0.3<br>ref_t = 323 323<br>; Pressure coupling = <br>Pcoupl = berendsen <br>Pcoupltype = semiisotropic<br>tau_p = 3.0 30<br>
compressibility = 3e-5 3e-5<br>ref_p = 1.0 1.0<br><br>constraints = none <br>constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br>
lincs_warnangle = 30<br><br><br><div class="gmail_quote">On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
Hi,<br><br>I am 99.99% sure that there is no problem with COM motion removal in Gromacs.<br>Could you post your mdp parameters?<br><br>Berk<br><br>> From: <a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a><br>
> To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center<br>> Date: Wed, 2 Sep 2009 16:04:39 +0200<div>
<div></div><div class="h5"><br>> <br>> <br>> I am not sure how to fix the trajectory that has drifted ...<br>> <br>> But if your bilayer drifts even if you use a removal of the COM for <br>> the water and<br>
> bilayer separately that means there is problem in the code! And this <br>> should be<br>> fixed.<br>> <br>> XAvier.<br>> <br>> On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:<br>> <br>> > Dear Experts<br>
> ><br>> > I had posted this earlier, but the problem was not solved by earlier <br>> > suggestions. So am posting again.<br>> ><br>> > I am simulating a POPC bilayer using MARTINI. The simulation ran <br>
> > fine, but the bilayer drifted towards the edge of the box along the <br>> > bilayer normal, and eventually some of the atoms crossed the box <br>> > boundaries. In some cases, entire lipid molecules crossed the box <br>
> > boundaries. I tried to recenter the trajectory, so that the lipid <br>> > bilayer would be at the center of the box at all times. But for some <br>> > reason, this does not seem to work? I have tried simulations using a <br>
> > single comm_group for the entire system, as well as separate ones <br>> > for the lipid and water, but the same problem appears in either case.<br>> ><br>> > Typically, for all-atom bilayers, the following set of commands <br>
> > works to correct the drift:<br>> ><br>> > #### first convert original trajectory to a temp. xtc ###<br>> > echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br>
> > #### then convert temp.xtc to the final trajecory ###<br>> > echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br>> ><br>> > where groups 3 and 0 are the lipid and the whole system <br>
> > respectively, and final.xtc is my final trajectory.<br>> ><br>> > However, this does not work for the MARTINI systems. Looking at the <br>> > final trajectory in VMD, the bilayer is either at the center of the <br>
> > box, or it is split at the box edges, with each monomer being in <br>> > different leaflets.<br>> ><br>> > If I plot the center of mass motion of the entire system in the <br>> > original trajectory .. the system seems to drift by ~ 2-3 angstroms <br>
> > in one direction. As a result, water center of mass drifts in the <br>> > opposite direction (because of PBC).<br>> ><br>> > Are there any suggestions to sort this out? One option is to write <br>
> > the entire trajectory to .gro files, recenter all of them (depending <br>> > upon whether the bilayer is in the center or is split at the box <br>> > edge), and concatenate the gro files again.but this is tedious, even <br>
> > if scripted.<br>> ><br>> > Please let me know if i can provide any additional info ?<br>> ><br>> > -- <br>> > Maria G.<br>> > Technical University of Denmark<br>> > Copenhagen<br>
> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before <br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>
Copenhagen<br>