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

XAvier Periole x.periole at rug.nl
Wed Sep 2 16:50:57 CEST 2009 

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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