[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
maria goranovic
mariagoranovic at gmail.com
Thu Sep 3 10:23:24 CEST 2009
Hi Berk,
Shorter tau_p? I thought you suggested 5.0 or 10.0 ps ?
On Wed, Sep 2, 2009 at 5:28 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> I also just recalled that we have a bug report open since two years already
> about drift of the COM:
> http://bugzilla.gromacs.org/show_bug.cgi?id=165
> But in that case double precision did not change anything, so that does not
> seem to be a precision issue.
> Here tau_p was 1 ps, but up till now we did not manage to find the source
> of this problem.
>
> Thus it would be useful to see if a shorter tau_p fixes it in your case.
>
> Berk
>
> ------------------------------
> Date: Wed, 2 Sep 2009 17:21:46 +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
>
> I will change the tau_p values, and report back. This might take more than
> a week though.
>
> maria
>
>
> On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess <gmx3 at hotmail.com> wrote:
>
> 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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> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
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>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
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--
Maria G.
Technical University of Denmark
Copenhagen
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