I attached the output files in my earlier reply. My molecule is somewaht
similar to plastocyanin as discussed in AMBER tutorial 4 instead of copper
I have a K+ ion (non -bonded interaction with monomer) , I have non bonded
parameters in my frcmod file while I construct the solvated box .
Is my error related to this intitial structure , I require to have a non
bonded ion, how can I work with this in the input files while running MD.
Thanks
Kirtana
On Sun, Dec 4, 2011 at 3:02 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > equilibration at 50K at constant
> > volume and then I turn on constant pressure equilibration
>
> Did you jump the temperature or change the time step between
> the two? I suggest pasting in all your mdin files to the response.
>
> Bill
>
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Received on Sun Dec 04 2011 - 12:30:04 PST
