[gmx-users] a box of water

Justin Lemkul jalemkul at vt.edu
Fri Sep 7 13:41:11 CEST 2012

On 9/7/12 7:34 AM, Turgay Cakmak wrote:
> Hi all,
> I want to do Molecular dynamics simulation of a box of water (SPC
> type). I get the spc216.pdb file from the gromacs/share/tutor.
> Firstly, I did geometry optimization for nsteps= 50000.
> Now, can I continue with production run or do I need to do
> equilibration runs to arrive correct temperature and pressure?

Equilibration is always advisable, though for a system of water you don't do any 
sort of position-restrained steps as you would if there were a solute.  In any 
case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out 
some of the beginning of the "production" trajectory anyway, since generation of 
velocities does not guarantee that you maintain any sort of equilibrated state, 
so the beginning of the run is equilibration.  For stability reasons, NVT and 
NPT are advisable.  Water is pretty robust, but why take a chance when 
equilibration steps are fast to do?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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