On 12/27/2011 7:44 PM, lina wrote:
Hi,
I met a very untamed simulation system.
when I tried to run a short MD, it's collapsed with LINCS Warnings,
It's under 317K
so I used energy minimizations after NVT, and run another NVT_2 again.
(In vacuum, no NPT being applied here).
after that NVT_2, mainly increased the steps, run MD, it's collapsed
again after 500ps,
so I used the energy minimization from that nvt_2.gro several times,
and it's collapsed during energy minimizations.
Might I used wrong way of handling it. I tried 300K, which can run a
bit further without collapse.
Thanks for any suggestions you may give.
Do I need to work hard on the energy minimization or?
The usual advice is here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System>.
Mark
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