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
incompatible.
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
file?
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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