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

Anirban Ghosh reach.anirban.ghosh at gmail.com
Wed Apr 28 13:11:41 CEST 2010

Hello Justin,

In my topology file I am declaring:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

; Strong position restraints on rest of B2AR
#include "strong_posre.itp"

; 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
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.



On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul <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
> 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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