From: Amit Paliwal (paliwal_at_jhu.edu)
Date: Wed Jan 07 2004 - 05:10:03 CST
> Thanks Jim and Jerome,
> That was indeed the case ...I will take that into account.
> -Amit.
>
> Jim Phillips wrote:
>
> > Hi,
> >
> > I suspect that your outputEnergies period (e.g., 10) is not a multiple of
> > your fullElectFrequency period (e.g., 4). The logic that avoids the extra
> > math to calculate ELECT energies that the user never sees doesn't
> > anticipate this, so half of the energy output are missing the long-range
> > ELECT energy component. The other energy terms should be OK.
> >
> > Minimization uses energies directly and therefore always calculates them.
> >
> > -Jim
> >
> > On Tue, 6 Jan 2004, AMIT PALIWAL wrote:
> >
> > > Hi everyone, I have had this problem with the new namd version 2.5.
> > > Whenever I simulate peptide in water- first minimize the system and then
> > > start the production run- in the production run, the total energy
> > > oscillates beween two levels very far apart. I can not understand why??
> > > Minimization seems to be perfectly fine. There was a suggestion to use
> > > separate thermostats for peptide and water. if this is the problem then
> > > how do you go about doing this? thanks, Amit.
> > >
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