[gmx-users] Structure blowing up after increased the temperature

Justin Lemkul jalemkul at vt.edu
Tue Mar 21 22:24:52 CET 2017

On 3/21/17 12:39 PM, Sameer Edirisinghe wrote:
> Dear users,
> I'm trying to find the melting point and Tg of my polymer system using
> Density vs temperature curve. I'm using all oplsaa forcefield and  I'm going
> for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each.
> then after the production run (at 523K for 5ns) the system is blowing up
> and can be observed broken molecules of the trajectory from VMD. But no
> blowing up occurring at 300K temperature (200ns).

"Broken" molecules are a consequence of PBC, not instability.

> But if I only did the production run (at 523K) up to 200ps it seems no
> blowing up occurring until 200ps.

Systems simulated at higher temperature will naturally diffuse faster, therefore 
cross periodic boundaries more frequently or more quickly.

> Note. used .mdp files has attached with the mail

The mailing list does not accept attachments.

> 1) I'm not sure if the .mdp files caused the blowing up or the topology
> caused the blow up of the system.
> 2) Can use same .mdp files by only changing coupling temperature for any
> temperature?

High-temperature simulations often require shorter time steps and perhaps a bit 
tighter regulation of temperature and pressure to be stable, but as of yet we 
have no evidence that your simulation was actually unstable.



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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