On 1/05/2012 12:20 PM, cuong nguyen wrote:
Thanks,
I tried to add -maxsol 846 to the command and got the box with 846
water molecules. However, when I use VMD to visualize the box, these
molecules concentrate on 1/3 the box space. I do need the molecules to
spread out whole box.
So next time think about asking the question whose answer you actually
want... Do some arithmetic and put a suitable box around a single water
molecule. Then replicate with genconf, like I suggested last time.
Mark
Cheers,
Cuong
2012/5/1 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
On 4/30/12 10:02 PM, cuong nguyen wrote:
Dear Gromacs Users,
I used the command "genbox -cs spc216.gro -o box1.g96 -p
topol.top -box 3 3 10"
to create box of 3010 water molecules. However, now I need to
create a same size
box with only 846 water molecules. Please help me to do this.
Use the -maxsol option when invoking genbox.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Nguyen Van Cuong
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