On Fri, Nov 23, 2012, subramanian boopathi wrote:
>
> i have run the first two minimization succefully completed
> for amyloid protein interact new molecule. These structure
> contains 163 atoms. Further i have been running the heating
> procedure from zero to 300 kelvin and dt =0.002 , nstlim=10000
> , while i have facing ETOT energy is shows as NAN , similar
> result for Restrain, EPOT, and etc. So i have decided to
> change the dt =0.0002 while heating process is running upto
> 4picosecond further vlimit and vexceed error shows following
> out put of heating process. can you please help me to overcome
> this problem. please say whether moving in the correct path.
There is something wrong with the potential energy surface you are using, but
it's not possible to figure out what that is from the information we have.
Are there non-standard parts to your system?
One good idea is to set ntwx=1 (or 2) and look at the trajectory you get,
especially concentrating on what happens when you start to get vlimit errors.
You can also use the "checkoverlap" command in ptraj to look for bad contacts.
...good luck...dac
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Received on Mon Nov 26 2012 - 05:30:02 PST
