vinothkumar mohanakrishnan wrote:
Hi justin
if genbox is not able to find sufficient space then why should one
calculate number density for the given box dimension?.similarly the the
Just because you can calculate a certain number density does not necessarily
mean that the algorithm genbox is using can produce such a configuration. It
inserts molecules randomly, so you may be able to find a magical value of -seed
for which this will work. The simpler approach is what I suggested earlier.
number of molecules are not getting updated in the molecules section of
the topology file when inserting multiple molecules using the genbox
command. everytime i need to update it manually.is <http://manually.is>
there a way to update it automatically?
The topology will only be updated automatically when adding water. Otherwise,
you have to do it yourself.
-Justin
Regards
Vinoth
On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
vinothkumar mohanakrishnan wrote:
Hi all
I have a diffculty in adding multiple molecules of hexane to my
box. my box size is 4.72*2.36*2.36 (nm) according to my number
density calculations the box should fit 124 molecules of hexane
whereas it adds only 76 molecules to the box below is my
command. i had evev tried with -try command but without sucess.
genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
hexane-multi.gro -nmol 124 -seed 1268
If you're not getting all the molecules you want, then genbox is
unable to find sufficient space for them. Try a larger box, then
equilibrate.
-Justin
Regards
Vinoth
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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