[gmx-users] high initial temperature with low ref_T

[Mark Abraham]

Dongsheng Zhang wrote:
> Dear Mark,
> 
> Do you have any idea what's wrong with my simulation? You can find the
> mdp file and the description how I set up my system at the bottom of
> this email. 

If you're trying to do vacuum simulations with infinite cutoffs and no 
periodicity, then the .mdp looks fine to me. I'm not sure from your 
description whether you did EM after introducing the CNT - obviously 
you'll need an EM .mdp file for that, not this one. You will want to do 
this before attempting to equilibrate the combined system.

If an EM and/or simulation with just the CNT explodes (using the .mdp 
files from the proven-good polymer simulation), then you'd be able to 
conclude your CNT topology is broken and you need to fix the .top file.

Mark