David van der Spoel wrote:
On 2012-03-09 17:10, saly jackson wrote:
Hi all
As Justin said to fill a box with 80000 molecules I should construct
small boxes containing for example some hundred molecules with 'genconf'
and then build a big box including 80000 molecules. Now I want to know
how can I use 'genconf' and then genbox, instead of the following
command (Only genbox)?
genbox -ci H.gro -nmol 80000 -box 300 300 300 -p topol.top -o H-box.gro
try a smaller box and then you can scale it using editconf if needed.
Rather than scaling with editconf (which can distort coordinates, in my
experience), one can also use genconf -nbox to replicate the smaller system, i.e.:
genconf -f small_box.gro -nbox 5 5 5 -o large_box.gro
which creates a system 125 times larger than the original. Adjust as needed.
-Justin
Would you please help me?
Thanks
Saly
--
========================================
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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