[gmx-users] Make an index file

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Apr 29 11:53:58 CEST 2012

Dear Mark,
Wow, That was kind of you.
I appreciate you.
Ok, I will try it.

 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, April 29, 2012 2:11 PM
Subject: Re: [gmx-users] Make an index file

On 29/04/2012 7:32 PM, Shima Arasteh wrote: 
Actually, I am confused somehow. 
>I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below.
>title        = NVT equilibration for POPC
>define        = -DPOSRES    ; position restrain the protein
>; Run parameters
>integrator    = md        ; leap-frog integrator
>nsteps        = 50000        ; 2 * 50000 = 100 ps
>dt            = 0.002        ; 2 fs
>; Output control
>nstxout        = 100        ; save coordinates every 0.2 ps
>nstvout        = 100        ; save velocities every 0.2 ps
>nstenergy    = 100        ; save energies every 0.2 ps
>nstlog        = 100        ; update log file every 0.2 ps
>; Bond parameters
>continuation    = no            ; first dynamics run
>constraint_algorithm = lincs    ; holonomic constraints 
>constraints    = all-bonds            ; all bonds (even
            heavy atom-H bonds) constrained
>lincs_iter    = 1                    ; accuracy of LINCS
>lincs_order    = 4                    ; also related to
>; Neighborsearching
>ns_type        = grid        ; search neighboring grid cels
>nstlist        = 5            ; 10 fs
>rlist        = 1.2        ; short-range neighborlist cutoff
            (in nm)
>rcoulomb    = 1.2        ; short-range electrostatic cutoff
            (in nm)
>rvdw        = 1.2        ; short-range van der Waals cutoff
            (in nm)
>; Electrostatics
>coulombtype    = PME        ; Particle Mesh Ewald for
            long-range electrostatics
>pme_order    = 4            ; cubic interpolation
>fourierspacing    = 0.16        ; grid spacing for FFT
>; Temperature coupling is on
>tcoupl        = V-rescale                ; modified
            Berendsen thermostat
>tc-grps        = POPC SOL    ; two coupling groups - more
Here you instruct grompp to expect the POPC group...

tau_t        = 0.1    0.1                ; time constant, in ps
>ref_t        = 323     323                ; reference
            temperature, one for each group, in K
>; Pressure coupling is off
>pcoupl        = no         ; no pressure coupling in NVT
>; Periodic boundary conditions
>pbc            = xyz        ; 3-D PBC
>; Dispersion correction
>DispCorr    = EnerPres    ; account for cut-off vdW scheme
>; Velocity generation
>gen_vel        = yes        ; assign velocities from Maxwell
>gen_temp    = 323        ; temperature for Maxwell
>gen_seed    = -1        ; generate a random seed
>I enter this command:
># grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr
>Getting this fatal error:
>Group POPC not found in index file.
>Group names must match either [moleculetype] names
>or custom index group names,in which case you
>must supply an index file to the '-n' option of grompp. 
>I don't need index file, do I?  What is the problem with my .mdp file?
... but POPC is not defined implicitly by your .top+.gro
    combination, nor explicitly in an index file supplied with grompp
    -n. AFAIK if your [moleculetype] is named POPC then it is all OK,
    but maybe the fact that your .gro file has the POPC "residues" named
    POP is confusing that mechanism. As you can see with your earlier
    example with make_ndx, the POP group is defined implicitly by the
    residue names in your .gro file, so if you use that output index
    file and reference POP in your .mdp file, all will be good. You
    might get away without using that index file, but I am not sure
    about this. Simpler still is to use Water and non-Water as your
    T-coupling groups, but this will need changing if down the road you
    need Protein as well (or such).


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