[gmx-users] question about dynamics

Shuangxing Dai shuangxingdai at gmail.com
Mon Jul 12 21:40:44 CEST 2010

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