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 <[email protected]> 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 <[email protected]> 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: [email protected] >> > To: [email protected] >> > 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 [email protected] >> > > 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 [email protected]. >> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > _______________________________________________ >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Maria G. > Technical University of Denmark > Copenhagen > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
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