Thanks! The problem was indeed the spaces in the group names.<br><br>Vaithee<br clear="all">=======================================================<br>S. Vaitheeswaran<br>Post-doctoral Research Associate<br>Center for Biotechnology and Interdisciplinary Studies<br>
Rensselaer Polytechnic Institute<br>110 8th Street, Troy NY 12180<br>Tel: 518-276-4245<br>email: <a href="mailto:vaiths@rpi.edu">vaiths@rpi.edu</a><br>=======================================================<br>
<br><br><div class="gmail_quote">On Fri, May 8, 2009 at 4:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
<div><div></div><div class="h5"><br>
<br>
S. Vaitheeswaran wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I am trying to calculate the PMF along the end-to-end distance for a short polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top, where sd.mdp is:<br>
************************<br>
title = cpp = /usr/bin/cpp<br>
integrator = sd<br>
dt = 0.002 ; [ps]<br>
nsteps = 1000000<br>
nstcomm = 10 ; frequency for center of mass motion removal<br>
comm_mode = Linear ; Remove center of mass translation<br>
comm_grps = system<br>
nstxtcout = 10000 ; frequency to write coordinates to xtc trajectory<br>
nstxout = 10000 ; frequency to write coordinates to output trajectory file<br>
nstvout = 100000<br>
nstlog = 10000<br>
nstenergy = 10000<br>
energygrps = 6EG ; group(s) to write to energy file<br>
pbc = no<br>
nstlist = 0 ; neighbor list is only constructed once and never updated.<br>
ns_type = simple<br>
rlist = 0 ; cut-off distance for the short-range neighbor list<br>
rcoulomb = 0<br>
rvdw = 0<br>
tc-grps = 6EG<br>
tau_t = 0.1 ; [ps]<br>
ref_t = 300 ; [K]<br>
pull = umbrella<br>
pull_geometry = distance<br>
pull_init1 = 0.425 ; [nm]<br>
pull_dim = Y Y Y<br>
pull_ngroups = 1<br>
pull_group0 = group 1<br>
pull_group1 = group 2<br>
pull_k1 = 1000<br>
************************<br>
group 1 and group 2 are defined in OH_ends.ndx:<br>
************************<br>
[ group 1 ]<br>
1 2<br>
[ group 2 ]<br>
20 21<br>
************************<br>
<br>
and 6EG.top is:<br>
************************<br>
#include "ffgmx.itp"<br>
#include "6EG.itp"<br>
[ system ]<br>
Hexa-ethylene glycol: Langevin dynamics<br>
[ molecules ]<br>
6EG 1<br>
************************<br>
<br>
But, grompp fails with:<br>
-------------------------------------------------------<br>
Program grompp_s, VERSION 4.0.4<br>
Source code file: readir.c, line: 1013<br>
<br>
Fatal error:<br>
Group 6EG not found in indexfile.<br>
Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>
In that case use the '-n' option.<br>
-------------------------------------------------------<br>
<br>
But, I *am* using the -n option! If I include the group 6EG in the index file (I didn't think it was necessary since it is defined in the .top file), grompp chokes with:<br>
"Fatal error: Group group 1 not found in indexfile.", even though group 1 is defined in the .ndx file. <br>
</blockquote>
<br></div></div>
Perhaps try taking the spaces out of the group names, i.e., group_1 and group_2.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
It works fine without the pulling options. I have searched the manual, wiki and mailing list archives for a solution, without success. This gromacs newbie is out of ideas -- any help is much appreciated.<br>
<br>
thanks,<br>
Vaithee<br>
<br>
<br></div>
------------------------------------------------------------------------<br>
<br>
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</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
</blockquote></div><br>