saly jackson wrote:
Hi all
I used genconf and genbox command as the following:
genconf -nbox 50 50 40 -f H.gro -nmolat 100 -o H-box.gro
How many molecules are in H.gro and H-box.gro? Is H.gro a single molecule?
genbox -cs H-box.gro -nmol 100000 -box 100 100 100 -p topol.top -o
H-box_new.gro
You've been advised again and again that building enormous systems in one step
will not work. This is not a robust approach, as your computer clearly doesn't
have the memory to handle it. Before you were trying to add 80000 molecules,
now 100000 certainly won't work. I doubt the combination of -cs and -nmol is
even sound in the first place.
Is there a particular reason you feel you need to construct a system containing
100000 molecules? Will a smaller, more manageable, system not suffice?
-Justin
But I received:
Reading solvent configuration
"Great Red Owns Many ACres of Sand "
solvent configuration contains 600000 atoms in 100000 residues
Killed
Would you please help me?
Thanks alot
Regards
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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