[gmx-users] Applying restraint onto Sodium Atoms
jalemkul at vt.edu
Thu May 8 03:47:39 CEST 2014
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
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
More information about the gromacs.org_gmx-users