[gmx-users] Water model used.

[Justin Lemkul]

On 8/26/14, 1:50 PM, Dawid das wrote:
> Dear Gromacs experts,
>
> Let's say that I use such an option in pdb2gmx:
> -water tip3p
>
> Then, while generating solvation box with genbox I use:
> -cs spc216.gro
>
> So my question is, what model do I actually use? SPC or TIP3P?
>

Whatever is in the topology.  SPC, SPC/E, and TIP3P are both 3-point models, so 
there's no need to keep around multiple 3-point coordinate files.  With just a 
bit of equilibration, everything is fine.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================