Hi Qian,
> Yes, what I ran is not a periodic boundary case. Actually I have
> already set nscm = 1000 but it still does not work. The coarse grained
> model I used is Ca-sidechain model, basically every amino acid is
> represented by two beads. The force field comes from a statistical
> potential. The coarse grained model should have a large conformational
> change than all-atom simulation. So is changing the size of the virtual
> box a solution to this error?
This sounds to me like your gradients are not correct and thus your system
is not conserving energy and thus momentum. Firstly try running a NVE
simulation and plot total energy (and temperature) vs time and see what it
looks like. It should be constant.
Second try comparing analytical and numerical gradients to make sure they
are correct. You can do this by using the debugf option.
title
&cntrl
...
...
/
&debugf
do_debugf=1,
atomn=1,2,3,4,5,6,7,8,9,10,
/
This should run a single energy evaluation and then calculate analytical vs
numerical derivatives. The difference in each case should be 10^-6 or less.
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 |
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Received on Mon May 23 2011 - 22:30:02 PDT
