[gmx-users] grompp in gromacs-4.0.4

[Justin A. Lemkul]

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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