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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