Hi everyone. I'm trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I've applied periodic boundary conditions and specified the box size. Does anyone know what I'm doing wrong? Thanks, Simon
Hi Simon, Sorry, no idea. You could try to see if anything looks weird with the atoms around that time, but without any error message we don’t have anything to go on. You could also try starting with a slightly different atom configuration, but it may not make any difference. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 13, 2019, at 2:39 AM, Simon Wheeler <simon.wheeler@dmu.ac.uk> wrote:
Hi everyone.
I’m trying to run an MD simulation in Chimera. It works with no thermostat and no barostat and it works with just a thermostat. But when I try to run it with a barostat it gets about 15% of the way through the equilibration stage and then Chimera hangs and the simulation never finishes. I’ve applied periodic boundary conditions and specified the box size. Does anyone know what I’m doing wrong? Thanks,
Simon _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng -
Simon Wheeler