[gmx-users] Please answer this!!! (Reaching the desired pressure and density)

Nima Sa nimavaeesa at yahoo.com
Mon Jul 13 00:17:44 CEST 2015

I'm sorry. I didn't mean to be ridiculous or selfish. I just wanted to be polite.Anyways, thanks for your comment. 

     On Sunday, July 12, 2015 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

Please don't use subject lines like this ("please help," "urgent," etc); it's a 
bit ridiculous.  You double-posted after waiting only a few hours on a weekend. 
  Be patient.  Free advice isn't a service you can demand.

On 7/12/15 4:37 AM, Nima Sa wrote:
> Hi, Dear users,I have created a box of polymer with about 50 molecules. I'm
> performing NPT runs to reach to the pressure of 1 bar. After a long time of
> simulation (15 ns) the average pressure is still about -0.5 and the density
> has saturated to around 700 kg/m^3 which should become 1200 kg/m^3 at the
> pressure of one bar. These are the related parameters in .mdp file: ;
> Pressure coupling is onpcoupl = berendsen ; Pressure coupling on in
> NPTpcoupltype = isotropic ; uniform scaling of box vectorstau_p = 0.2 ; time
> constant, in psref_p = 1.0 ; reference pressure, in barcompressibility =
> 4.5e-5 ; isothermal compressibility of water, bar^-1 Does anyone know how can
> I fix this? Which parameters should I change to reach the desired pressure
> and density?Thanks in advance.-Nima Azar

15 ns is not a long time, especially with complex systems like polymers.  And, 
as I just told someone else, if the model doesn't produce the correct physical 
behavior, it's entirely possible that the force field parameters are inadequate.



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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