Hi David,
Sorry, actually I was running NVT simulations actually.
Best,
Mo
On Thu, Sep 20, 2012 at 12:10 PM, Mo Chen <mc842.cornell.edu> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Sep 20 2012 - 10:00:03 PDT
