[gmx-users] a box of water

Turgay Cakmak turgaycakmak34 at gmail.com
Fri Sep 7 13:52:08 CEST 2012

Thanks a lot for your quick reply Justin. I got it.

2012/9/7 Justin Lemkul <jalemkul at vt.edu>:
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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