jampani srinivas wrote:
Hi
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.
I haven't been following this closely; can you post an .mdp file?
-Justin
Thanks in advance.
Srinivas.
On Wed, Apr 7, 2010 at 4:47 PM, ms <deviceran...@gmail.com
<mailto:deviceran...@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
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Drexel University
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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