[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 20 18:45:36 CET 2012

Anik Sen wrote:
> Respected Sir,
>                      I am new to gromacs. Am using GROMACS 4.5.5 
> version. I have two questions..
> 1.  I want to know about plotting the co-ordination number (CN) of the 
> water molecules around one of my substrate say a KCl molecule for 
> example. What should i do to get the CN number.

There are extensive discussions on this topic in the list archive, including 
possible use of RDF or other software.  I'd suggest you search for this information.

> 2. I have three different substrates. I want to create a same box size 
> irrespective of the size of my molecule and generate same number of 
> water molecules around them. What should I do?

I doubt you can have both.  For a given box size, if the solute molecule 
occupies a different volume, then less water molecules will fit in the box.  If 
you limit the number of water molecules around your smallest solvent in the 
given box, you will have voids within the box that will either collapse under 
NPT (leading to the box size decreasing) or will cause the formation of small 
vacuum pockets under NVT (which is not realistic in the condensed phase, obviously).

You can obtain either using editconf -box (to define a particular box size) or 
genbox -maxsol (to set a maximum value of solvent).  Whether or not you can 
accomplish what you want in a sound manner (or whether it is even necessary) is 



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


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