Hi,
When I used Amber10 to simulate protein folding, I obtained the following error message:
system extended beyond the virtual box
All energys recorded in the last frame are normal. I checked the mailing list and someone said this error message is related to the non-bond list. So I set nsnb=1000000000, which is equal to my nstlim. But it did not solve the problem. My simulation is a coarse-grained simulation so the conformation should have a large fluctuaion. Is this the problem to cause the error? Can I change the size of the virtual box to a large value, like 100 Angstroms? Or there are other solutions. Thanks a lot.
Sincerely,
Qian
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Received on Mon May 23 2011 - 20:30:03 PDT
