[gmx-users] position restrain

[pragya chohan]

Thanks for your help. My simulation ran with your idea.
----------------------------------------
> Date: Thu, 15 Nov 2007 13:34:40 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] position restrain
> 
> If you read the documentation for genpr, it tells you that it will only generate
> a position restraint file for the first molecule, so grompp is telling you that
> only the protein is being restrained, which is what you should expect.  If you
> really insist on restraining the water molecules, try reading about the
> freezegrps options for your .mdp file, but doing so will typically cause
> problems if you are using pressure coupling.
> 
> -Justin
> 
> Quoting pragya chohan <pragyachohan at hotmail.com>:
> 
> >
> > hi
> > I have a system of protein, popc,water and Cl ions. I want to position
> > restrain protein and water as without position restrain water is going into
> > the membrane . So I made a group of protein and water together using make_ndx
> > and then genpr. When i ran grompp i got the following error:
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 3.3
> > Source code file: toppush.c, line: 1108
> >
> > Fatal error:
> > [ file "posre1.itp", line 582 ]:
> >              Atom index (5362) in position_restraints out of bounds (1-577)
> >
> > The commands i used are:
> > make_ndx -f em_dpt_popc.gro -o
> >  0 System              : 12663 atoms
> >   1 Protein             :   577 atoms
> >   2 Protein-H           :   456 atoms
> >   3 C-alpha             :    59 atoms
> >   4 Backbone            :   177 atoms
> >   5 MainChain           :   237 atoms
> >   6 MainChain+Cb        :   294 atoms
> >   7 MainChain+H         :   296 atoms
> >   8 SideChain           :   281 atoms
> >   9 SideChain-H         :   219 atoms
> >  10 Prot-Masses         :   577 atoms
> >  11 Non-Protein         : 12086 atoms
> >  12 POPC                :  4784 atoms
> >  13 SOL                 :  7299 atoms
> >  14 Cl                  :     3 atoms
> >  15 Other               : 12086 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
> >
> > > 1|13
> >
> > Copied index group 1 'Protein'
> > Copied index group 13 'SOL'
> > Merged two groups with OR: 577 7299 -> 7876
> >
> >  16 Protein_SOL         :  7876 atoms
> >
> > > q
> >
> > genpr -f em_dpt_popc.gro -o posre1 -n index.ndx
> >
> > Group    16 ( Protein_SOL) has  7876 elements
> > Select a group: 16
> > Selected 16: 'Protein_SOL'
> >
> > grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o
> > pr_dpt_popc
> >
> > What is the best way to do this? Please suggest.
> > _________________________________________________________________
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> 
> 
> 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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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