[gmx-users] Re: Holes in the solvent!

Justin Lemkul jalemkul at vt.edu
Mon Oct 29 14:41:19 CET 2012

On 10/29/12 9:38 AM, Arman Mahboubi Soufiani wrote:
> Dear Friends,
> Thank you for your kind and informative responses. As Dr. Chaban noted, I
> checked the density and it was roughly 880 gr.cm-3 which seems low!
> I greatly appreciate your further helps.

Most water models underestimate water density, so that is likely a contributing 
factor.  You haven't told us much about your setup, so it's hard to guess what 
you should be expecting.  You also haven't said how large your polymer is in 
relation to the size of the box, so that could affect the outcome, as well.  A 
picture showing these "holes" would also be useful, as they very well could be a 
PBC effect and thus totally normal.  From your description, I was assuming the 
holes were within the solvent, but if they are at the box "edges" then likely 
what you are seeing is normal.



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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