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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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