[gmx-users] energy minimization problem

[soumadwip ghosh]

Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?

Here is how the CNT molecule looks like prior to energy minimization.

pre energy min CNT
<https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing>

I am not continuing any of the equilibration steps anymore. As you can see
the CNT structure is distorted badly.

Please help me out. What settings do I need to change in order to avoid
such distortion? Is there a possibility that the cnt topology was wrong to
begin with?

Regards,
Soumadwip
Research Fellow
IITB
India