[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 17:06:50 CEST 2009
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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