Hi Junjun
> Thanks a lot to all of you. Now I understand more. As Bob and Bill
> pointed
> out, the ele is calculated for those outside the cut when PME is
> enabled, I
> agree with what Mike mentioned that vdw is quite small at the cut.
> However,
> in case of vacuum simulation, is there any different algorithms to deal
> with
> the electrostatics that moves out of the cutoff? If there isn't, there
> seems
> to be a convergence problem in vacuum simulation when cut isn't large.
Sander was never really designed to be used for vacuum simulations (and
pmemd does not allow it) hence it does not have anything to deal with the
situation of energy conservation in gas phase simulations. For example there
is no switching or shifting functions in sander. You may be getting confused
here with skinnb thinking that it is related to a switching function, e.g.
like charmm has cutofnb, cutonnb, cutnb etc. I always forget which is which.
In Sander (and pmemd) the skinnb is purely part of the list building
heuristic and does not affect the actual cutoff in any way, which is always
square at cut (or square adjusted by erfc in the case of pme / ewald calcs).
Thus when running gas phase simulations you should typically always run with
no cut off (cut=9999.0) if you want to conserve energy. Of course you should
also be aware that the force fields were never actually developed with gas
phase simulations in mind.
> that sander stops rebuilding the nonbond list during the whole
> simulation.
>
> What I found surprises me. The vacuum simulation ran 100 MD steps
> without
> updating the nblist.
This is to be expected. You told the code never to update the nonbond list
so it doesn't.
> The potential energy was going all the way to more
> negative values and the temperature was going all the way to higher
> values. The temperature was 600 K at the 100 step.
> Can anybody please explain this?
Your system is probably very unstable in this configuration so is dumping
potential energy into kinetic energy and giving you a higher and higher
temperature.
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Wed May 12 2010 - 20:30:03 PDT
