[gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

[Justin Lemkul]

On 6/6/17 2:34 AM, Apramita Chand wrote:
> Dear Andre,
> I added around 56 molecules of urea to 966 water. The peptide is just 6
> residues and I just wanted to see its preferred conformations as well as
> hydrogen bonding.
> I will definitely try to extend the simulation to atleast 100ns.
> For the equilibration, I found that the temperature and pressure had
> converged to its desired values within 10ns. Why do we need to give longer
> equilbration times?
> 

Getting the temperature and pressure to converge is a simple matter that is 
often achieved within a few hundred ps.  It does not mean you are at equilibrium 
sampling with respect to the properties of your system.  You need to do 
convergence checks of all the relevant quantities (peptide properties, 
distribution of the co-solvents, H-bonding, etc).

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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