On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
Thank Tsjerk so much !
But after being minimized 50000 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ? or minimize many
times ? to get more equilibrated system.
I would say that 50000 steps of minimization is far more than is normally
necessary. What Fmax do you achieve at the end of EM? What is in the system?
What is in your .mdp file? Systems can randomly crash if the model physics
breaks due to incorrect .mdp settings or an unstable topology.
-Justin
On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <[email protected]>wrote:
Hi KT,
This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <[email protected]
wrote:
Dear All,
My MD simulation has an error
Warning: Only triclinic boxes with the first vector parallel to the
x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
I searched on Gromacs-errors web, but i did not see this error.
How can i fix it ?
Thanks and regards,
KT
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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