[gmx-users] grompp in gromacs-4.0.4

[S. Vaitheeswaran]

Thanks!  The problem was indeed the spaces in the group names.

Vaithee
=======================================================
S. Vaitheeswaran
Post-doctoral Research Associate
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
110 8th Street, Troy NY 12180
Tel: 518-276-4245
email: vaiths at rpi.edu
=======================================================


On Fri, May 8, 2009 at 4:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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