VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Nov 16 2016 - 08:57:32 CST

Dear Raviteja,
You can use SPC/E just by making appropriate topology/parameter files.
If you want to use autoionize with SPC/E, it is probably easier to just build the system with TIP3 and then change the residue names, atom names/types, and charges afterwards (or rebuild the psf once all the ions are in place).
The watermodel argument in the config file is only needed when you want a water model with special internal constraints (e.g., the massless charge site in TIP4). SPC/E doesn’t require any special handling and can thus be dealt with at the level of the topology/parameters.
Best,
Peter

> On Nov 16, 2016, at 7:18 AM, Raviteja Kurapati <tsii.ravi_at_gmail.com> wrote:
>
> 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