[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

Berk Hess gmx3 at hotmail.com
Wed Sep 2 17:16:23 CEST 2009

```It might actually affect the center of mass motion removal,
because you would be scaling your system with 1 +- 1 bit at every step.
This could produce consistent rounding in one direction in single precision,
causing the system to move in one direction.

This is something we should check in general.
Often people are using too small tau_p values, like 0.5 or 1 ps,
so I advise them to use 5 or 10 ps.
But if larger values cause problems in single precision we should be aware
of this.

Could you report back if changing tau_p solves the drifting problem?

Berk

Date: Wed, 2 Sep 2009 17:06:50 +0200
Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory 	so that the bilayer is at the center
From: mariagoranovic at gmail.com
To: gmx-users at gromacs.org

Oh dear. That is not good. the missing decimal point in tau_p it is a typo all right. but it seems i have used it in the simulations too. thank you for noticing, Xavier.

that forces  redoing a lot of simulations.

that said, it should still not impact the center of mass removal anyway?

-maria

On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole <x.periole at rug.nl> wrote:

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 <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
> > _______________________________________________
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--
Maria G.
Technical University of Denmark

Copenhagen

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