[gmx-users] Applying restraint onto Sodium Atoms

[Justin Lemkul]

On 5/7/14, 5:05 PM, Carlos Navarrro Retamal wrote:
> Hi everyone,
> I’m trying to perform a MD simulations of a LEA (late embryogenesis abundant) protein on different solvents with different water contents.  Our protein doesn’t have a neutral charge, so we have to add also 6 sodiums ions. When we use a system with just a few water molecules (500 and even less), the sodium ions start to interact with the protein and this one starts to fold around the ions in by adopting and non-standar  conformation.
> So basically, my question is: Is there a way to apply a force (restraint) onto this 6 ions in order to avoid any kind of strange interactions between our protein and the different sodium ions?

Yes, it's quite straightforward to modify ions.itp to include conditional 
position restraints exactly like one might do for water (see #ifdef POSRES_WATER 
block written by pdb2gmx in your protein .top file).  The bigger question is 
what sort of artifacts might arise because of these restraints.  If you're 
seeing clustering of ions near the protein (presumably within some thin 
solvation shell), that indicates significant repulsion from whatever else is in 
the system.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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