Samuel Silva Pita wrote:
Hi all,
my problem in my "by hand' topology remains until now but the errors in atoms
of solvent added through genbox command at GMX 3.3.1 disappeared. Unfortnately the
variable ci is giving me some headaches and because this I cannot do my topology.
Can someone help me in this type of problem? Thanks for your tips Esther but the
problem continues to boring me!
Thanks all in advance!!
please start from scratch and describe your problem again. normally this
means poor minimization. if you write a solvent topology by hand you
should first minimize and simulate a single molecule before making a liquid.
****************************************************
Program mdrun_331, VERSION 3.3.1
Source code file:nsgrid.c, line: 226
range checking error:
Explanation: During neighborsearching, we assign each particle to a grid based
on its coordinates. If your system contains errors that give particles very
high velocities you might end up with some coordinates being +- Infinity ou NaN
********************************************************
"Do not wear yourself out to get rich;do not trust your own cleverness. Cast but a
glance at riches, and they are gone, for they will surely sprout wings and fly off to the
sky like an eagle."(Proverbs 23:4-5)
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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