[gmx-users] Re: NEMD

Mark Abraham 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:
>     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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