Hi Amir,
> > Dear Dr. Case,
> > As you said i put the nstlim =100 and ntpr =1. in this
> case,simulation run successfully but when i increase the nstlim thats
> problem came back! in mdout file nothing was wrong!
> > what should I Do?
> >
> Dear Dr.Case,
> I found that when ions in my system increased sticking of simulation
> occurred more. why? and what should i do?
I think you need to define EXACTLY what you mean by the term sticking. We
will also need significantly more information about your simulation, how you
are setting it up, what your input files look like, what version of AMBER
are you using, is it patched with the latest bugfixes, what is the command
line, how are you running the calculation? On a cluster through a queuing
system, on your desktop etc? - If a queuing system what does your submission
script look like etc.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 28 2012 - 10:00:03 PST
