VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Mar 29 2018 - 12:28:40 CDT

Hi Alex,

You make them yourself. Here is an example to make a box of 1000 methanol.

package require psfgen
topology /home/josh/toppar/top_all36_cgenff.rtf
#Segment QQQ is essential if you want to use VMD solvate.
segment QQQ {
    for { set i 0 } { $i < 1000 } { incr i } {
        residue $i MEOH
    }
}
regenerate angles dihedrals
writepsf meoh.psf
exit

Then you'd come up with some way of populating coordinates for 1000 of
your molecules. I like using insert-molecules from the GROMACS
simulation suite:

gmx insert-molecules -ci onemethanol.pdb -o meoh.pdb -nmol 1000 -box 8 8 8

You can also assign coordinates by script within the psf. It is just
more work than insert-molecules. Then you'd put it together and run
simulation under constant pressure to get the right density, and use the
solvate plugin, using the optional -spdb, -spsf and -stop options.
(http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/)

-Josh

On 03/29/2018 11:01 AM, Alex Saad-Falcon wrote:
> Hello all,
>
> How can I find PDB and PSF files for non-water solvents? Ideally, I
> want a range of pH values from ~6.5-8.5, but any help on where to find
> a solvent other than water would be greatly appreciated.
>
> Thanks,
>
> Alex