Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ?

From: Erdem Yeler <erdemyeler.gmail.com>
Date: Fri, 26 Jun 2020 20:50:47 +0300

I changed the ntx parameter (as ntx=5) but nothing changed. I couldn't find
my mistake. Any suggestions? Still I couldn't understand why my simulation
looks like normal but energies are restarting at every 500 steps.

Erdem Yeler <erdemyeler.gmail.com>, 12 Haz 2020 Cum, 19:49 tarihinde şunu
yazdı:

> Dear David, thanks for your help and reply. Here is my mdin file:
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000, dt = 0.0022
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
>
>
> David A Case <david.case.rutgers.edu>, 8 Haz 2020 Pzt, 03:31 tarihinde
> şunu yazdı:
>
>> On Mon, Jun 08, 2020, Erdem Yeler wrote:
>>
>> > actually I couldn't find my mdin file. it was deleted by the
>> >administrator of the server after the job was finished.But I copied all
>> >files from the tutorial I mentioned above. I am doing multiple runs.
>>
>> I've lost track of what the "tutorial I mentioned above" is. Are you
>> running separate jobs, each of 500 steps? It really sounds (as others
>> have suggested) that somehow you are not updating the files correctly.
>>
>> If you have an mdout (output) file, the mdin file is listed at the top
>> of that file. But we also need to know exactly what the command line
>> arguments you are using. Those are also printed in the mdout file. So,
>> examining carefully what is in the mdout file, and posting it if you
>> can't find anything wrong, might be the next step.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 26 2020 - 11:00:03 PDT
Custom Search