Why don't you do energy minimization? It's pretty clear that you've generated
some atomic overlap in your procedure, from what you've described.
For general reference on such problems, check the hundreds of related posts
(LINCS warnings) in the list archive or the following link to the wiki site
Dear users,
I have a problem on running MD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system. My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other)
1. editconf -f lc -bt d -box 1.3 0
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