[gmx-users] nvt equilibration

[Justin Lemkul]

On 6/4/15 5:26 AM, marzieh dehghan wrote:
> Hi
>
> thank you for your answer
>
> I used the following instructions: make_ndx -f em.gro -o index.ndx
>
> and appear thses text:
>
> Reading structure file
> Going to read 0 old index file(s)
>
> Analysing residue names:
> There are:   421      Other residues
> There are:  4446      Water residues
> There are:    10        Ion residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
>    0 System              : 13871 atoms
>    1 Other               :   523 atoms
>    2 UNK                 :   523 atoms
>    3 CL                  :    10 atoms
>    4 Water               : 13338 atoms
>    5 SOL                 : 13338 atoms
>    6 non-Water           :   533 atoms
>    7 Ion                 :    10 atoms
>    8 UNK                 :   523 atoms
>    9 CL                  :    10 atoms
>   10 Water_and_ions      : 13348 atoms
>
>   nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>   'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>   't': atom type   |   'keep' nr        'splitat' nr    'h': help
>   'r': residue         'res' nr         'chain' char
>   "name": group        'case': case sensitive           'q': save and quit
>   'ri': residue index
>

Please provide your full .mdp file.  You've got lots of people guessing at what 
you're trying to do and they're all referring to different things.  What groups 
are you trying to create, and why?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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