S. Vaitheeswaran wrote:
Dear gromacs users,
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:
************************
title =
cpp = /usr/bin/cpp
integrator = sd
dt = 0.002 ; [ps]
nsteps = 1000000
nstcomm = 10 ; frequency for center of mass motion removal
comm_mode = Linear ; Remove center of mass translation
comm_grps = system
nstxtcout = 10000 ; frequency to write coordinates to xtc
trajectory
nstxout = 10000 ; frequency to write coordinates to output
trajectory file
nstvout = 100000
nstlog = 10000
nstenergy = 10000
energygrps = 6EG ; group(s) to write to energy file
pbc = no
nstlist = 0 ; neighbor list is only constructed once
and never updated.
ns_type = simple
rlist = 0 ; cut-off distance for the short-range
neighbor list
rcoulomb = 0
rvdw = 0
tc-grps = 6EG
tau_t = 0.1 ; [ps]
ref_t = 300 ; [K]
pull = umbrella
pull_geometry = distance
pull_init1 = 0.425 ; [nm]
pull_dim = Y Y Y
pull_ngroups = 1
pull_group0 = group 1
pull_group1 = group 2
pull_k1 = 1000
************************
group 1 and group 2 are defined in OH_ends.ndx:
************************
[ group 1 ]
1 2
[ group 2 ]
20 21
************************
and 6EG.top is:
************************
#include "ffgmx.itp"
#include "6EG.itp"
[ system ]
Hexa-ethylene glycol: Langevin dynamics
[ molecules ]
6EG 1
************************
But, grompp fails with:
-------------------------------------------------------
Program grompp_s, VERSION 4.0.4
Source code file: readir.c, line: 1013
Fatal error:
Group 6EG not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.
-------------------------------------------------------
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:
"Fatal error: Group group 1 not found in indexfile.", even though group
1 is defined in the .ndx file.
Perhaps try taking the spaces out of the group names, i.e., group_1 and group_2.
-Justin
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.
thanks,
Vaithee
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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