[gmx-users] problem with total energy

jampani srinivas jampanis at gmail.com
Thu Apr 8 15:22:28 CEST 2010


Thanks for your response, I am allowing the two groups (frozen and
non-frozen) groups interact each other, i guess i am getting the energy of
total system from g_energy.

I checked the velocities of frozen group atoms, they are not "zero". I have
seen in git master that this problem was fixed and updated in md.c file, I
have downloaded this from git master and compiled my gromacs again still i
found that frozen atoms gets the initial velocity.

I am not at all clear why the energy of system should blow up, can you
please help me if there is solution for this.

Thanks in advance.


On Wed, Apr 7, 2010 at 4:47 PM, ms <devicerandom at gmail.com> wrote:

> jampani srinivas ha scritto:
> > Dear Berk,
> >
> > I am sorry if i am confusing you with my poor description of problem,
> > actually I have submitted simulation with two temperature coupling groups
> (i
> > think you already know that from our earlier conversations) and found
> that
> > there is a continuous increase in the total energy of the system. I could
> > not observe any blowing in the output file but the system energy is
> > continuously increasing, i am using 4fs time step here. Can you please
> let
> > me know if i have to give more details?
> >
> Which part of the system is increasing its energy?
> m.
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J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off:     215-895-1989
       Mob:  704-706-4191
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