[gmx-developers] Re: Pull code and virial
mbx0009 at yahoo.com
Tue Mar 1 22:40:56 CET 2005
--- Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> Justin MacCallum wrote:
> >> I guess the best way to fix this would be to calculate the pull virial
> >> (also for constraint pulling)
> >> in the pull code, store it in the forcerec and add it in calc_virial,
> >> just as is done
> >> for the grid part of the electrostatics virial.
> > That sounds very reasonable to me. I'll leave it to you though as I am
> > not at all familiar with code that does the virial calculations in
> > GROMACS.
> I have implemented the virial correction for afm and umbrella pulling.
> But I have noticed that the afm and umbrella pull code is not correct.
> The forces are only applied to the 'other' groups, not to the reference
> So the system is no longer Newtonian and one can not check things
> such as energy conservation.
reminds me of a problem i had a while ago with the pull code,
it turned out that frozen atoms DO move when they are part
of a pulled group (or the reference group)... and i seem to recall
that that problem was resoved a short while ago, possibly something
went wrong there ...
be that as it may, if you change the code please do not
forget to account for frozen atoms (which are rather un-physical
anyway, and therefore energy conservation is probably not
a big issue in such a case)
> When there is no absolute reference I have now also added minus the force
> to the reference group and now we have energy conservation and zero average
> virial for pulling on two atoms with charge.
> I would consider this force problem a pretty serious error.
> I don't know how others think about it.
> If there are no objections, I will commit tomorrow.
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