[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
maria goranovic
mariagoranovic at gmail.com
Wed Sep 2 16:45:05 CEST 2009
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 <gmx3 at hotmail.com> 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: x.periole at rug.nl
> > To: gmx-users at gromacs.org
> > 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 gmx-users at gromacs.org
> > > 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 gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> > 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 gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090902/9384d8b5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list