[gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

Justin Lemkul jalemkul at vt.edu
Mon Oct 13 13:36:50 CEST 2014

On 10/13/14 4:48 AM, liuyong_1007 at dicp.ac.cn wrote:
> Dear gromacs usres,
> I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase (vacuum) at higher temperature ( bigger than 200 K).
> But the cluster will collapse at high temperature. So the distance restraints is used to restraint the water molecules and the ion Na+ not to keep together as a cluster.
> But there are so many atoms to set the distance constraint in the topology. So how can I set set the distance constraint in the topology easilier?
> How to set the distance restraint between the atoms and center of mass of the water-ion cluster?

The spherical flat-bottom potential is much easier to use in this case.  See 
manual section 4.3.2 (version 5.0).



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


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