your second value for tau_p is missing the "." is this a typo?
On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:
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 <g...@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.peri...@rug.nl
> To: gmx-users@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
> > _______________________________________________
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> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
Maria G.
Technical University of Denmark
Copenhagen
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