[gmx-users] problem with freezing group size

jampani srinivas jampanis at gmail.com
Thu Feb 25 16:09:08 CET 2010

Dear all,

I am sorry for poorly describing my problem about the freezing group size.
Here I am giving my question very briefly, can anybody help me please?

I would like to know the relation between the size of freezing group and the
temperature coupling. when I separate the temperature coupling for freezing
and non freezing groups the initial temperature for whole system is showing
me zero in the log file, and the non-freezing group is just vibrating not at
all moving during the course of simulation. This is true only when I am
using large freezing group (freezing group has 26540 atoms and non-freezing
group has around 9000 atoms). However if I use small freezing group
(freezing group has 7340 atoms and non-freezing group has around 25840
atoms) I am getting log file with initial temperature as 300K, and the
non-freezing group is moving well and the diffusion coefficient of solvent
is matching with its corresponding value in the bulk (with out freezing).

I hope somebody understand my problem now!!! thanks very much.

Thanks in advance

J. Srinivasa Rao
Post-doctoral Research Associate
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104
Ph:  Off:     215-895-1989
       Mob:  704-706-4191
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