[gmx-users] Variable ci yet!

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 9 20:51:37 CEST 2006

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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