I will change the tau_p values, and report back. This might take more than a week though.<br><br>maria<br><br><br><div class="gmail_quote">On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
It might actually affect the center of mass motion removal,<br>because you would be scaling your system with 1 +- 1 bit at every step.<br>This could produce consistent rounding in one direction in single precision,<br>causing the system to move in one direction.<br>
<br>This is something we should check in general.<br>Often people are using too small tau_p values, like 0.5 or 1 ps,<br>so I advise them to use 5 or 10 ps.<br>But if larger values cause problems in single precision we should be aware<br>
of this.<br><br>Could you report back if changing tau_p solves the drifting problem?<br><br>Berk<br><br><hr>Date: Wed, 2 Sep 2009 17:06:50 +0200<div class="im"><br>Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center<br>
</div>From: <a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a><div><div></div><div class="h5"><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>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. <br><br>that forces redoing a lot of simulations. <br>
<br>that said, it should still not impact the center of mass removal anyway? <br><br>-maria<br><br><div>On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote style="padding-left: 1ex;"><div><div><br></div>your second value for tau_p is missing the "." is this a typo?<div>
<div></div><div><div><br><div><div>On Sep 2, 2009, at 4:45 PM, maria goranovic wrote:</div><br><blockquote>Here are the mdp parameters:<br><br><br>title = POPC<br>cpp = /usr/bin/cpp<br>
integrator = md<br>tinit = 0.0<br>dt = 0.030<br> nsteps = 3000000<br>nstcomm = 1<br>comm-grps = Lipid W<br><br>; OUTPUT CONTROL OPTIONS = <br>
; Output frequency for coords (x), velocities (v) and forces (f) = <br>nstxout = 30000<br> nstvout = 30000<br>nstfout = 0<br>nstlog = 30000<br>nstenergy = 30000<br>
<br>ns_type = grid<br>nstlist = 10<br>pbc = xyz<br> rlist = 1.2<br><br>; Method for doing electrostatics = <br>coulombtype = Shift <br>
rcoulomb_switch = 0.0<br>rcoulomb = 1.2<br>epsilon_r = 15<br>vdw_type = Shift <br> ; cut-off lengths = <br>rvdw_switch = 0.9<br>rvdw = 1.2<br>
DispCorr = No<br><br>; Temperature coupling = <br>tcoupl = Berendsen<br>tc-grps = Lipid W<br> tau_t = 0.3 0.3<br>ref_t = 323 323<br>
; Pressure coupling = <br>Pcoupl = berendsen <br>Pcoupltype = semiisotropic<br>tau_p = 3.0 30<br> compressibility = 3e-5 3e-5<br>ref_p = 1.0 1.0<br>
<br>constraints = none <br>constraint_algorithm = Lincs<br>unconstrained_start = no<br>lincs_order = 4<br> lincs_warnangle = 30<br><br><br><div>On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="padding-left: 1ex;"> <div> Hi,<br><br>I am 99.99% sure that there is no problem with COM motion removal in Gromacs.<br>
Could you post your mdp parameters?<br><br>Berk<br><br>> From: <a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a><br> > To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center<br>> Date: Wed, 2 Sep 2009 16:04:39 +0200<div> <div></div><div><br>> <br>> <br>> I am not sure how to fix the trajectory that has drifted ...<br>
> <br>> But if your bilayer drifts even if you use a removal of the COM for <br>> the water and<br> > bilayer separately that means there is problem in the code! And this <br>> should be<br>> fixed.<br>
> <br>> XAvier.<br>> <br>> On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:<br>> <br>> > Dear Experts<br> > ><br>> > I had posted this earlier, but the problem was not solved by earlier <br>
> > suggestions. So am posting again.<br>> ><br>> > I am simulating a POPC bilayer using MARTINI. The simulation ran <br> > > fine, but the bilayer drifted towards the edge of the box along the <br>
> > bilayer normal, and eventually some of the atoms crossed the box <br>> > boundaries. In some cases, entire lipid molecules crossed the box <br> > > boundaries. I tried to recenter the trajectory, so that the lipid <br>
> > bilayer would be at the center of the box at all times. But for some <br>> > reason, this does not seem to work? I have tried simulations using a <br> > > single comm_group for the entire system, as well as separate ones <br>
> > for the lipid and water, but the same problem appears in either case.<br>> ><br>> > Typically, for all-atom bilayers, the following set of commands <br> > > works to correct the drift:<br>> ><br>
> > #### first convert original trajectory to a temp. xtc ###<br>> > echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br> > > #### then convert temp.xtc to the final trajecory ###<br>
> > echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br>> ><br>> > where groups 3 and 0 are the lipid and the whole system <br> > > respectively, and final.xtc is my final trajectory.<br>
> ><br>> > However, this does not work for the MARTINI systems. Looking at the <br>> > final trajectory in VMD, the bilayer is either at the center of the <br> > > box, or it is split at the box edges, with each monomer being in <br>
> > different leaflets.<br>> ><br>> > If I plot the center of mass motion of the entire system in the <br>> > original trajectory .. the system seems to drift by ~ 2-3 angstroms <br> > > in one direction. As a result, water center of mass drifts in the <br>
> > opposite direction (because of PBC).<br>> ><br>> > Are there any suggestions to sort this out? One option is to write <br> > > the entire trajectory to .gro files, recenter all of them (depending <br>
> > upon whether the bilayer is in the center or is split at the box <br>> > edge), and concatenate the gro files again.but this is tedious, even <br> > > if scripted.<br>> ><br>> > Please let me know if i can provide any additional info ?<br>
> ><br>> > -- <br>> > Maria G.<br>> > Technical University of Denmark<br>> > Copenhagen<br> > > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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