[gmx-users] WHAT TO DO WITH BAD CONTACTS?

[Mark Abraham]

Hi,

Please don't write your email subject (or text!) in capital letters. 
It's considered the internet equivalent of shouting.

> Hi  all,
> I did a simulation of unusual protein in pure methanol for 1 ns but in 
> final results there was a bad contact of methanol molecule (no. 508) 
> with carbonyl oxygen of the acetyl group of  the N terminal. I was 
> trying to remove this particular molecule and wanted to extend the run 
> but same problem of character coding of .trr and .tpr file. But I do not 
> want to start the fresh run of 1 ns because other methanol molecule will 
> take its place. In extending of run there is need of these two files. 

I don't know what makes you think this methanol is a "bad contact" since 
you haven't elaborated your reasons, but it sounds like you're trying to 
fix the symptoms of the problem, and not the cause.

In any case there's no way to do what you want, since that would require 
re-equilibration. Once you're re-equilibrating, you may as well start a 
new simulation entirely.

Mark