On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur <manik.ma...@gmail.com> wrote:
> > > 2009/3/17 Berk Hess <g...@hotmail.com> > >> Hi, >> >> You pull rate is ridiculously high (1 nm/ps). >> > Also I am simulating in reduced dimentions. I think it is fine then. 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: manik.ma...@gmail.com >> To: gmx-users@gromacs.org >> 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Graduate student > Microfluidics Lab > Dept. of Mechanical Engg. > IIT Kharagpur > -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
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