[gmx-users] simulation a box of water

Justin Lemkul jalemkul at vt.edu
Wed Mar 16 17:04:45 CET 2016

On 3/16/16 12:00 PM, Saeed Nasiri wrote:
> thanks so much for all the comments.
> as far as I know the water molecules created by models have solid bods and
> angles. I want to extract thermodynamical parameters from the simulation,
> for this purpose I used this method.
> Is this a trick to used water molecule explicitly?

If I understand the question, you simply want to carry out a simulation of 
flexible water?  You still need to choose a water model (for charges, LJ, and 
bonded parameters) but you can run with "define = -DFLEXIBLE" to avoid the use 
of SETTLE, which keeps the model rigid.  Inspect the contents of any water 
model's .itp file and you will see exactly what's going on.  Moreover, you don't 
need pdb2gmx, because the topology is straightforward to write by hand:

#include (some force field)
#include (the water model's .itp file)

[ system ]

[ molecules ]
SOL	3000

That's it.  People tend to get hung up on this idea that you have to use 
pdb2gmx.  That's not true at all, especially for utterly trivial systems like 
this one.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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