[gmx-users] bond lost!
Mark.Abraham at anu.edu.au
Mon Sep 18 07:37:51 CEST 2006
> good everyone
> i have 2 questions :
> 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for
> 5000steps,but it stopped at 467th step,and i found the conformation
> break,8chains'lost the C-OH bonds,why there was this and what cause
> this?was this the wrong itp or mdp?
Your topology was not correct. Compare the contents of the .top file
with the .itp file it was sourced from.
> 2) when i change the mdp with md,then show the gro atomnumber not
> incorred with top?why?i still could not find out the reason!
I can't understand this. You need to describe the problem fully, include
contents of small files where appropriate, and quote the feedback you
get from the gromacs tools. Or you could employ a mind-reader. I know
what's cheaper :-)
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