[gmx-users] Problem with Position Restraints (before running SMD)!

[Justin A. Lemkul]

Talal E. AlOtaibi wrote:
> Thank you so much Justin,
>  
> I made some changes and the SMD run was fine with no errors but I 
> still have the same problem (the fixed points moved away from their 
> original position).
>  

How great is the displacement?  Recall what I said before - position restraints 
are simply a bias against change, they do not prevent the change in position. 
If your pulling force is stronger than the restraining force, motion occurs and 
Newton was right ;)

I mentioned two possible fixes before.  If the displacement is unacceptably 
large, try those suggestions.

> I made index file for the atoms that i want to fix. Then, I use 
> 'genrestr' to generate 'posre.itp' file that contains the 
> [position_restraints] points. After that, I add the following to the 
> Topology file:
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> Then, I run my SMD simulation. But, I get the same problem. Could you 
> please tell me what is my problem. I really try to do my best.
> BTW, I didn't find any example in wiki that could help me to run SMD 
> simulation that contains both fix points and points under load.
>  

There is no such example.  I was pointing you to the proper method for 
#including position restraints directives in a complex topology.

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

> Thanks alot,
> Talal
>  > Date: Thu, 19 Jan 2012 10:39:30 -0500
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] Problem with Position Restraints (before 
> running SMD)!
>  >
>  >
>  >
>  > Talal E. AlOtaibi wrote:
>  >
>  > >
>  > > ; Position restraint for each water oxygen
>  > > [ position_restraints ]
>  > > ; i funct       fcx        fcy        fcz
>  > > 1 1 1000 1000 1000
>  > > 1330 1 1000 1000 1000
>  > > 1426 1 1000 1000 1000
>  > > 1437 1 1000 1000 1000
>  > > 1548 1 1000 1000 1000
>  > >
>  > > #endif
>  >
>  > More to the point, this will fail and should have raised a fatal 
> error in
>  > grompp. You're putting restraints on atoms that can't possibly exist 
> in water.
>  > The numbering is done per [moleculetype] so a position restraint 
> directive for
>  > water can only have numbers 1, 2, and 3 (OW and the two HW atoms).
>  >
>  > If you're trying to restrain atoms in a protein, you have to create a 
> separate
>  > [position_restraints] directive within the protein's [moleculetype]. 
> See the
>  > wiki for an example.
>  >
>  > -Justin
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================