On 15/08/2012 10:27 PM, mohammad agha wrote:
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic
Hi Sara,
The number of molecules in your .gro file and .top file should be the same.
That means when you want to add 12000 solvent molecules, change the number of
solvent molecules in your topology file to 12000. The total number of your
solvent and solute molecules in you topology and
On 14/08/2012 5:27 PM, mohammad agha wrote:
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
What's it? genbox? grompp? You can't be helped effectively if you
don't provide your command lines that produce output, and/or a
description of
On 14/08/2012 6:55 PM, mohammad agha wrote:
Dear Mark,
Thank you very much from your help.
I used from genbox to place solvent molecules. my question is : In the NPT
ensemble, for equilibrium, may the box become smaller than definite sizes
before equilibrium(for example 2nm become smaller)
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