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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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