[gmx-users] question about dynamics

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 12 21:43:27 CEST 2010

Shuangxing Dai wrote:
> Hi, all:
>     I am studying thermal expansion of bulk crystal solid. I want to 
> reach the state with 300K in temperature and 1 bar pressure.  I am not 
> sure whether my procedure is correct or not.
>     First I run energy minimization, then a constant volume for 
> temperature coupling ( integrator is sd), then run with Berendson for 
> anisotropic pressure coupling for 50 ps, then run anisotropic pressure 
> coupling using Panello-Rahman for 10 ps, finally a constant volume step 
> for production for 10 ps.
>     I do not know whether this procedure is correct or not.  Also, since 
> for my small system, fluctuation is very large, so is there any way to 
> reach the state ( 300K and 1 bar) and the system is fully in equilibrium?

The timeframes you're using are extremely short.  I'd suspect that it would be 
hard to get any system, especially a small one prone to large fluctuations, in 
an equilibrium state in 70 ps total.  Simple equilibration of a protein in water 
is typically done for no less than 100 ps per ensemble.

>     Also, I got a question about the ,mdp file options. When I use md 
> integrator, with Nose-Hover for temperature coupling and Panello-Rahman 
> pressure coupling, there is no error information. When I change and use 
> Berendson for pressure coupling, there is error information and does not 
> work.

Well, what's the error?  This kind of description will get you no useful advice.


>    Anyone have idea about these? Thanks in advance.
> Thanks,
> Shuangxing Dai


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list