[gmx-users] exploding system

[lina]

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?

Best regards,


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Re: [gmx-users] exploding system

[Mark Abraham]

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 
.


Mark

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