[gmx-users] bond lost!

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 18 07:37:51 CEST 2006

zzhwise1 wrote:
> 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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