[gmx-users] Please guide me

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> I am not sure.
> How can I check it?
> I think as you.but I don't know what and how can I modify it.

Look at the .log file for any indication of whether or not the job is still 
running.  Check the .edr and .xtc files with gmxcheck to see how many frames 
they contain.

-Justin

> 
> On Thu, Oct 14, 2010 at 1:52 PM, ms <devicerandom at gmail.com 
> <mailto:devicerandom at gmail.com>> wrote:
> 
>     On 14/10/10 08:51, mohsen ramezanpour wrote:
> 
>         Dear All
> 
>         I am running a seamulated anneaking + MD in my cluster.
>         I had done it for 2 times.
>         but my results are not as i expect.
>         I have attached my md.mdp file for you,I don't know which part
>         of it is
>         wrong.
>         what i like to result is to change tempreture from 420 in 0 ps
>         to 450 in 20
>         ps and then gradually lowering tempreture to 300 in 850 ps.and
>         this fix tempreture by the end of simulation.
>         but all of my result who I extract T-plot of them show me just
>         untill 2 ps.
>         then it is incomplete.
> 
> 
>     Are you sure your simulation doesn't crash?
> 
> 
>         Really I don't know what I must to do.
>         Please let me know my wrong.
>         Please guid me and edit my md.mdp file for this foal if it is
>         possivle.
>         I am waiting for your reply
>         Thanks oin advance for your reply
> 
>         Sincerely
>         Mohsen
> 
> 
> 
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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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