[gmx-users] NPT, freezegroups and Position Restraints.

Justin Lemkul jalemkul at vt.edu
Mon Aug 19 17:35:21 CEST 2013

On 8/19/13 11:32 AM, HANNIBAL LECTER wrote:
> Hi,
> I have been performing NPT simulations with CNT, Protein and water.
> However, when I freeze the CNT, the system crashes with segmentation fault.

That is to be expected.  Frozen atoms and pressure coupling are fundamentally 

> If I use position restraints, the temperature of the system is lower than
> what it is expected to be. I am using sd coupling.
> If I couple the protein, CNT and SOL separately, the temperature of the
> peptide is lower than 300K (~395K) while the temperature of the CNT is
> 157K. The target temperature is 300K in all cases. Can any please explain
> why such discrepancies are occurring?

Are these temperatures from g_energy or g_traj?  Can you please post a full .mdp 



Justin A. Lemkul, Ph.D.
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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