[gmx-users] protein membrane system

Justin Lemkul jalemkul at vt.edu
Tue Dec 25 23:41:50 CET 2012

On 12/25/12 12:53 PM, Shima Arasteh wrote:
> In order to compare the first and the second .gro file, I used grep -c OW (file.gro) to see how many waters exist in my new system. I got 22352, however I got 23703 before ( when I had not deleted the disturbing water molecules). So 23703-22352=1351 molecules.
> Also I compared the atom noumbers in two .gro files( .gro files : before and after deleteing disturbing water molecules):
> Before: 103723
> After: 99625
> Then 103723-99652=4071 divided by 3 gets: 1357 molecules.
> There is a difference between 2 answer. 6 molecules! What's wrong? I am sure that I have just deleted water molecules by VMD.
> Any body helps me  please?

Be more careful about what you delete and be sure that you have deleted whole 
molecules.  As I pointed out before, your water molecules appear to be off by a 
single atom, indicating incomplete deletion of at least one molecule.



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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