2009/3/17 Berk Hess <[email protected]> > Hi, > > You pull rate is ridiculously high (1 nm/ps). >
Is there any upper limit on the pull rate? btw are the other parameters consistent with the system I am trying to simulate? > Berk > > > ------------------------------ > Date: Tue, 17 Mar 2009 19:54:50 +0530 > From: [email protected] > To: [email protected] > Subject: [gmx-users] mdrun hangs with the pull option > > > Hi, > I am trying to simulate a case where I am pulling a set of atoms with > constant velocity with respect to another set of atoms, like: > > XXXXXXXXXXXXXXXXXXXXXXXXXXX --> U (velocity, moving wall, pull group) > ooooooooooooooooooooooooooo > ooooooooooooooooooooooooooo -> fluid > ooooooooooooooooooooooooooo > XXXXXXXXXXXXXXXXXXXXXXXXXXX --> fixed wall (reference group) > > but while running mdrun for the case, it simply becomes unresponsive after > 300 steps (no output message even with the -v option). Can somebody suggest > what I might be missing. I am appending the md.log and .mdp file for > reference however, for quick reference the excerpts are-> > > *) eql.mdp: > > ; COM PULLING > ; Pull type: no, umbrella, constraint or constant_force > pull = constraint > pull_geometry = direction > pull_start = yes > pull_init = > pull_nstxout = 10 > pull_ngroups = 1 > pull_group0 = WD > pull_group1 = WU > pull_vec1 = 1 0 0 > pull_rate1 = 1 > > *) md.log: > > pull = constraint > pull_geometry = direction > pull_dim (3): > pull_dim[0]=1 > pull_dim[1]=1 > pull_dim[2]=1 > pull_r1 = 1 > pull_r0 = 1.5 > pull_constr_tol = 1e-06 > pull_nstxout = 10 > pull_nstfout = 1 > pull_ngrp = 1 > pull_group 0: > atom (672): > atom[0,...,671] = {672,...,1343} > weight: not available > pbcatom = 1007 > vec (3): > vec[0]= 0.00000e+00 > vec[1]= 0.00000e+00 > vec[2]= 0.00000e+00 > init (3): > init[0]= 0.00000e+00 > init[1]= 0.00000e+00 > init[2]= 0.00000e+00 > rate = 0 > k = 0 > kB = 0 > pull_group 1: > atom (672): > atom[0,...,671] = {0,...,671} > weight: not available > pbcatom = 335 > vec (3): > vec[0]= 1.00000e+00 > vec[1]= 0.00000e+00 > vec[2]= 0.00000e+00 > init (3): > init[0]= 2.08088e+00 > init[1]= 0.00000e+00 > init[2]= 0.00000e+00 > rate = 1 > k = 0 > kB = 0 > > The other useful data might be: > OS- Ubuntu 8.04 > Gromacs- 4.0.2 > > Thanks, > Manik Mayur > -- > Graduate student > Microfluidics Lab > Dept. of Mechanical Engg. > IIT Kharagpur > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
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