[gmx-users] Distance restrain with dummy atom
jalemkul at vt.edu
Tue Aug 11 16:07:03 CEST 2015
On 8/11/15 8:30 AM, anu chandra wrote:
> Dear Gromacs users,
> I am working with membrane simulations and I would like to put distance
> restrain along Z-axis between a dummy atom I generated at the centre of box
> and all the water molecules. For this, I first generated a dummy atom at
> the centre of box and also made a simple .itp file for it as shown below,
> [ moleculetype ]
> ; molname nrexcl
> DUM 1
> [ atoms ]
> ; id at type res nr residu name at name cg nr charge
> 1 MW 1 DUM DUM 0 0 1
> I am using charmm36 ff and atom type MW is special dummy particle mention
> in the charmm36 ffnonbonded.itp file, as shown below.
> ; special dummy-type particles
> MNH3 0 0.000000 0.00 A 0.0 0.0
> MNH2 0 0.000000 0.00 A 0.0 0.0
> MCH3 0 0.000000 0.00 A 0.0 0.0
> MCH3S 0 0.000000 0.00 A 0.0 0.0
> *MW *
> * 0 0.000000 0.00 A 0.0 0.0*
> Am I doing it correct here, for generating a dummy atom? Am I doing correct
> with provide hydrogen mass to dummy atom?
> Few other queries regarding the distance restrain are,
> 1. How do I make sure that the dummy atom do not fly away from the centre
> of box?
> 2. What steps I should take to generate a file for distance restrain
> between dummy atom and water molecules?
> Please help me to clarify these queries. Waiting for your valuable reply.
The better approach is to use the pull code, rather than layering on all this
complexity. But perhaps the ultimate question is - why do you need to restrain
all the waters to be within some distance of the membrane?
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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