Hi David,
I have run NVE simulations for the system. Below is my input file. May I
ask if you think there is still a problem? Thank you!
Sample pulling input
&cntrl
nstlim=10000000, cut=12.0,
ntpr=1000, ntwx=1000, ntt=3, gamma_ln=1.0,
imin=0, ntx=7, irest=1, ig = -1,
ntb=1, ntc=2, ntf=2, tol=0.00001,
dt=0.002, tempi=363., temp0=363.
/
&ewald vdwmeth=0 /
/
END
eof
Best,
Mo
On Thu, Sep 20, 2012 at 8:56 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Sep 18, 2012, Mo Chen wrote:
>
> > I am running Langevin dynamics simulations (ntt=3) for organic solvent
> > using Amber 11, and would like to calculate the self-diffusion
> coefficient
>
> Just a note: diffusion properties will be messed up by the use of (almost
> any) thermostat. So you should not expect the results to be physically
> meaningful. If you want to study dynamics, you need to run NVE
> simulations.
>
> ...dac
>
>
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Received on Thu Sep 20 2012 - 09:30:03 PDT
