[gmx-users] Holes in the solvent!

[Dallas Warren]

My suggestion would be that this is a periodic boundary condition artifact, what you are seeing is the holes in the solvent due to a chain protruding out of the opposite face of the simulation box.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Justin Lemkul
> Sent: Saturday, 27 October 2012 11:25 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Holes in the solvent!
> 
> 
> 
> On 10/26/12 3:25 PM, Arman M. Soufiani wrote:
> > Dear Gromacs users,
> >
> > I am simulating a protein on a polymer surface for further adsorption
> free
> > energy calculation.
> > However, after performing the NVT run either for short or long
> durations I
> > found out that couple of holes appear in the physiological saline
> solution
> > (solvent)!!!
> > Additionally, even proceeding with a long NPT run the holes are still
> > present in the system.
> > I would be thankful if you could direct me what could be source of
> such a
> > strange outcome.
> >
> 
> That sounds very odd, but perhaps your unit cell is not sufficiently
> solvated to
> start with.  If you have voids, you may have available volume.
> 
> -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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