Hi, Ross:
Thanks for correcting my mistakes.
I was wondering also how a water box with periodic boundaries could be
used for the implicit solvent MD. I didn’t understand the ‘DNA’ tutorial
quite well. In this tutorial, three .prmtop files are generated. The one
used for implicit solvent MD actually does not have any water molecular.
Now I understand that ‘implicit solvent’ means no solvent but includes
solvent effects within the force field equations. I don’t have anyone at
my end who knows the molecular dynamic. I learn all these by reading,
practicing and by my mistakes. Thank you for being patient to me.
> What is the ,o, here???
It is a typing mistake. Sorry. I use Window to do the remote access and
can save the files. So I re-typed the files.
> Try setting ntpr=1 and you will see that your calculation is not
frozen,
EGB routine is not very efficient with >1000 atoms or so.
Thank you very much for all your advice.
Regards
Bo
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Received on Mon Nov 29 2004 - 00:53:01 PST
