Re: TIP4P water box

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Feb 19 2019 - 21:03:02 CST

This has been discussed many times on the namd mailing list. See, for
example,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/2303.html
for some pre-equilibrated TIP4 boxes, which can be used with solvate (as a
nonstandard solvent). You could also just change the residue names on your
TIP3 water and rerun psfgen, using the topology files in the tarball linked
at the old post noted above. But one way or another, you need to actually
have complete TIP4 waters (including lone pair particles); it is not
sufficient to just set the water model to tip4.
Best,
Peter

On Tue, Feb 19, 2019 at 3:15 PM 김민재 <kjh950429_at_gmail.com> wrote:

> Hi everyone.
>
> I am currently trying to run a MD simulation with TIP4P water. I am
> relatively new to this. So, I followed the namd tutorial to solvate
> carbonic anhydrase in a water box (5 angstroms longer than the atoms with
> the highest coordinates in the x,y, and z axes.) However, in the resulting
> pdb file, I noticed that the water was TIP3. Would it still be okay to run
> the simulation with the configuration set to "waterModel tip4"? If not, how
> can I create a waterbox with TIP4 water?
>
> Thanks
>

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