[gmx-users] Problem with T-coupling.

Justin Lemkul jalemkul at vt.edu
Tue Jun 3 02:06:10 CEST 2014

On 6/2/14, 7:59 PM, Udaya Dahal wrote:
> Hi,
> I was simulating the PPO, n=27 chain in water. Currently I am simulating
> only single chain and so far the phase behavior and he h-bond looks good
> for the higher temperature but as I go to the lower temperature (293K and
> 298K), I expected to get little extended  structure unlike the coiled
> structure at higher temperature.
> But the problem, I am facing here is not the conformation but the overall
> simulation. I changed from berendsen T-coupling to nose-hoover and
> berendsen P-coupling to Parrinello-Rahman pressure coupling. When I see the
> trajectory in VMD, the trajectory of Berendsen thermostat and barostat
> looks like liquid but the nose-hoover and Parrinello-Rahman looks like
> freezing for the same system.
> When i checked the temperature from g_energy, it shows the coupling
> temperature. Could you please tell me what's wrong in the simulation?
> I have attached the .mdp file here with the email in google drive.​
>   eq.mdp
> <https://docs.google.com/file/d/0ByXdaXpbCwOyUVJuOFZ4dFBaa1U/edit?usp=drive_web>
> ​This one is for Berendsen T coupling.
>>   eq_nh.mdp
> <https://docs.google.com/file/d/0ByXdaXpbCwOySnBIa2tLRkFPZGc/edit?usp=drive_web>
> ​This one is for Nose-hoover.

You're using dissimilar nonbonded settings, thermostatting approaches, and plain 
cutoffs for Coulombic interactions.  The latter leads to junk simulations, and 
your observed freezing is consistent with a flying ice cube artifact.  Develop a 
robust, consistent protocol before trying to assign blame to the thermostats. 
Right now, the outcome could be due to any number of factors.



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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