[gmx-users] Re: NEMD
Mark.Abraham at anu.edu.au
Sat Nov 13 16:48:09 CET 2010
On 14/11/2010 2:42 AM, Junqiao Lee wrote:
> 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.
Is the starting configuration stable under normal MD?
> On Sat, Nov 13, 2010 at 11:17 PM, Junqiao Lee <aeondrift at gmail.com
> <mailto:aeondrift at gmail.com>> wrote:
> 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
> 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.
> Junqiao LEE (Wade)
> Curtin University
> Dept. of Chem. [NRI]
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