VMD-L Mailing List
From: Raviteja Kurapati (tsii.ravi_at_gmail.com)
Date: Wed Nov 16 2016 - 06:18:33 CST
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Hi,
I wish to use a spce water model with opls foce field for my simulation.
I am using modified tip3p pdb file (which comes with vmd) to generate psf
from str file provided at http://mackerell.umaryland.edu/charmm_ff.shtml in
c32b1 zip.
When I solvate using this newly made pdb-psf, the total no of water
molecules shows to be 9261 irrespective of box dimensions i put in solvate
plugin or tcl script.
Also I found it impossible to use autoionize plugin to balance the charge
when I name the residue SPCE instead of TIP3.
I also read that it is possible to mention water model used in conf file.
Can you please let me know how.
Thanks,
Raviteja
- Next message: Jérôme Hénin: "Fast PBC wrapping in VMD"
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- Reply: Peter Freddolino: "Re: which water models are inbult in namd? can I use SPCE if yes how?"
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