Hi Qian,
I assume you are running a gas phase or implicit solvent simulation here
rather than a periodic one yes?
What has happened is that your system is drifting, likely due to it having a
net center of mass translational motion. Unchecked this would ultimately
overflow the output files so needs to be addressed. The simplest approach is
to set nscm=1000 to periodically remove center of mass motion. This should
hopefully stop your system drifting away from the starting point.
Of course is you have modified the potential in some way and your gradients
are incorrect then your system will no longer preserve angular momentum or
linear momentum therefore you will have all sorts of problems. You do not
specify exactly what you mean by coarse grain simulation, which method,
force field etc so it is hard to know if anything was modified. I would
begin by setting nscm=1000 and see if this helps.
Good luck,
Ross
> -----Original Message-----
> From: Qian Wang [mailto:qwang.mail.uh.edu]
> Sent: Monday, May 23, 2011 8:29 PM
> To: amber.ambermd.org
> Subject: [AMBER] system extended beyond the virtual box
>
> 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 - 21:00:03 PDT
