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
--
========================================
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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