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 <g...@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: mariagorano...@gmail.com > > To: gmx-users@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.peri...@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 <g...@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.peri...@rug.nl > > To: gmx-users@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 > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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