[gmx-users] Re: NEMD

Junqiao Lee aeondrift at gmail.com
Sat Nov 13 16:42:43 CET 2010

Running the simulation in NVT doesn't seem to work too.

And (other than the system not blowing up now) similar to the NPT
simulations, both 2CosZ*Vel-X and 1/Viscosity that I've got out of the test
runs were 0.

On Sat, Nov 13, 2010 at 11:17 PM, Junqiao Lee <aeondrift at gmail.com> wrote:

> Hi,
> I've tried running an NEMD run in NPT vis setting the "cos_acceleration =
> 0.3" parameter to determine the solvent viscosity.
> However my system kept spectacularly exploding.
> I've also tried running with the acc_grps specified for 7 molecules (out of
> the 250 within the system), but it still didn't work.
> cos_acceleration = ~0.3 nm ps^-2 seem like a reasonable value to use?
> Am I only restricted to running NEMD calcs. in NVT?
> Thanks for the help.
> Cheers,
> Junqiao LEE (Wade)
> Curtin University
> Dept. of Chem. [NRI]
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