[gmx-users] problem with total energy

[Justin A. Lemkul]

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 <devicerandom at gmail.com 
> <mailto: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
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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