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Posted By: shane yue VVER+Nose in asymmetric unit simulation - 01/10/15 04:29 PM
Hi!

When I used the "Quick MD Simulator" of CHARMM-GUI to generator input files for asymmetric unit simulation of a crystal. I noticed that in both equilibration and production run inputs, VVER+Nose is used. Can anyone tell me why CHARMM-GUI chooses VVER+Nose rather then CPT+Hoover? Is there any special consideration in crystal simulation that makes VVER+Nose a better choice?

BTW, when I run simulation in NVT ensemble, I use "pcon pmass 0 ...".


Thanks in advance

Best
Posted By: rmv Re: VVER+Nose in asymmetric unit simulation - 01/10/15 05:32 PM
We've tended to avoid VVER, as it does not support constant P nor compute the virial. Another issue has been the difficulty in verifying the conservation of energy, as it's never been clear how to obtain the time series of the system Hamiltonian. Indeed, these issues led other developers to implement an alternative velocity Verlet integrator, VV2, which is needed for the Drude polarizable force fields.

I suppose VVER/NOSE may be okay, but it would be my third choice.
Hi Rick,

Thanks for your kind reply. I'll test CPT+Hoover to learn the difference. You have a nice day!

Best
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