[gmx-users] Freezing a portion of a protein during simulation

[Justin A. Lemkul]

Anirban Ghosh wrote:
> Hello Justin,
> 
> In my topology file I am declaring:
> ---------------------------------------------------------------------------------------------------------------
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Strong position restraints on rest of B2AR
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
> 

What is in strong_posre.itp?  Presumably you're only restraining certain 
residues, right?  Did you create this with genrestr and an appropriate index group?

> ; Include water topology
> #include "spc.itp"
> -----------------------------------------------------------------------------------------------------------------
> And in my .mdp file I am giving:
> -----------------------------------------------------------------------------------------------------------------
> define           = -DSTRONG_POSRES    
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 5000          ; 2 * 50000 = 100 ps
> dt                 = 0.002         ; 2 fs
> -------------------------------------------------------------------------------------------------------------------

If this is the entirety of your .mdp file, you're asking for trouble.  Allowing 
all other parameters to be taken as default is very dangerous, and probably 
inappropriate (most notably cutoff electrostatics).

> But now what I am getting is that if I run MD using these restraints on 
> the helical portion of the protein, then I am getting LINCS errors. 
> However, if I allow the entire protein to move during MD, then it is 
> running fine. What mistake am I making? And how can I freeze properly 
> the helical portions and simulate only the loop? Thanks a lot in advance.
> 

Recognize that there is a difference between "freezing" and "restraining."  Read 
in the manual about what freezing is versus position restraints.  Either way, 
you should be able to get things up and running, but position restraints are a 
bit easier to implement.

If an unrestrained simulation runs fine (using that fragmented .mdp file?) then 
there are probably just bad clashes in the system that the restraints are not 
allowing to relax.

-Justin

> Regards,
> 
> Anirban
> 
> On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Anirban Ghosh wrote:
> 
>         Hi ALL,
> 
>         I want to do a MD simulation by restraining (freezing) the
>         helical portions and allowing only the loop regions to move. I
>         tried doing this by applying heavy restrain on the helical
>         residues by generating a .itp file with the "genrestr" command
>         with an index file containing the desired residue numbers.
>         However during the simulation I am finding that the entire
>         protein is moving. Am I doing anything wrong? Or is there any
>         other way to freeze a portion of a protein? Any suggestion is
>         welcome. thanks a lot in advance.
> 
> 
>     If your protein is still moving, then you aren't correctly applying
>     your position restraints.  Without seeing your topology and .mdp
>     file, there's no way to know what you're doing wrong.
> 
>     You can also use the freezegrps option in the .mdp file, but then
>     you also have to make sure you're using the appropriate
>     energygrp_excl, etc.  It is generally much easier to apply position
>     restraints.
> 
>     -Justin
> 
> 
>         Regards,
> 
>         Anirban
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://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

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