VMD-L Mailing List

From: Christopher Gaughan (cgaughan_at_engzyme.net)
Date: Mon Jan 25 2021 - 02:05:51 CST

Hello all,

VMD has always just...WORKED for me and I just don't understand what the
problem is. I performed my simulation on XSEDE - Comet using pmemd-cuda. On
viewing the simulation system (the summary_ETOT, etc) All looks perfectly
well. Furthermore the simulated system is merely a 9 aa peptide with TIP3P
Water shell- not a very compex system. I gradually heated the system to
310K with no apparent problems.Then I ran a 60ps production run. I
downloaded the prod.nc and the peptide.top and fed them into VMD as per
usual. Note I am on a MAC running Big Sur v11.1.

Can anyone advise me on how to troubleshoot this?

Thanks
Chris