<br><br><div class="gmail_quote">On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur <span dir="ltr"><<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.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;">
<br><br><div class="gmail_quote">2009/3/17 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span><div class="im"><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Hi,<br><br>You pull rate is ridiculously high (1 nm/ps).</div></blockquote></div></div></blockquote><div class="gmail_quote"><div><br>Also I am simulating in reduced dimentions. I think it is fine then.<br><br></div></div>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="gmail_quote"><div>Is there any upper limit on the pull rate?<br>btw are the other parameters consistent with the system I am trying to simulate?<br>
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<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><div><br>Berk<br> <br><br><hr>Date: Tue, 17 Mar 2009 19:54:50 +0530<br>
From: <a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>Subject: [gmx-users] mdrun hangs with the pull option<div><div></div><div><br><br>Hi,<br>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:<br>
<br>XXXXXXXXXXXXXXXXXXXXXXXXXXX --> U (velocity, moving wall, pull group)<br>
ooooooooooooooooooooooooooo<br>ooooooooooooooooooooooooooo -> fluid<br>ooooooooooooooooooooooooooo<br>XXXXXXXXXXXXXXXXXXXXXXXXXXX --> fixed wall (reference group)<br><br>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-><br>
<br>*) eql.mdp:<br><br>; COM PULLING <br>; Pull type: no, umbrella, constraint or constant_force<br>pull = constraint<br>pull_geometry = direction<br>pull_start = yes<br>pull_init = <br>
pull_nstxout = 10<br>pull_ngroups = 1<br>pull_group0 = WD<br>pull_group1 = WU<br>pull_vec1 = 1 0 0<br>pull_rate1 = 1<br><br>*) md.log:<br><br>pull = constraint<br>
pull_geometry = direction<br> pull_dim (3):<br> pull_dim[0]=1<br> pull_dim[1]=1<br> pull_dim[2]=1<br> pull_r1 = 1<br> pull_r0 = 1.5<br> pull_constr_tol = 1e-06<br>
pull_nstxout = 10<br> pull_nstfout = 1<br> pull_ngrp = 1<br> pull_group 0:<br> atom (672):<br> atom[0,...,671] = {672,...,1343}<br> weight: not available<br> pbcatom = 1007<br>
vec (3):<br> vec[0]= 0.00000e+00<br> vec[1]= 0.00000e+00<br> vec[2]= 0.00000e+00<br> init (3):<br> init[0]= 0.00000e+00<br> init[1]= 0.00000e+00<br> init[2]= 0.00000e+00<br>
rate = 0<br> k = 0<br> kB = 0<br> pull_group 1:<br> atom (672):<br> atom[0,...,671] = {0,...,671}<br> weight: not available<br> pbcatom = 335<br>
vec (3):<br> vec[0]= 1.00000e+00<br> vec[1]= 0.00000e+00<br> vec[2]= 0.00000e+00<br> init (3):<br> init[0]= 2.08088e+00<br> init[1]= 0.00000e+00<br> init[2]= 0.00000e+00<br>
rate = 1<br> k = 0<br> kB = 0<br><br>The other useful data might be:<br>OS- Ubuntu 8.04<br>Gromacs- 4.0.2<br clear="all"><br>Thanks,<br>Manik Mayur<br>-- <br>
Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br><br></div></div><div><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a></div>
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-- <br>Graduate student<br>Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>IIT Kharagpur<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>