Re: restarting issue

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Fri Oct 10 2008 - 15:00:36 CDT

So, you mean this comes from the randomness of Langevin Dynamics. I see.
Thanks a lot.

Bin

On Oct 10, 2008, at 12:53 PM, Joshua Adelman wrote:

> Are you using a thermostat? If this is the case and you are
> concerned that you restart the simulation and you get a different
> result, then you need to take a look at the manual and see how the
> thermostat is implemented in namd.
>
> Josh
>
>
> On Oct 10, 2008, at 12:42 PM, BIN ZHANG wrote:
>
>> Hi, All:
>>
>> I was trying to restart my simulation, and found that the
>> result is quite different from previous calculation:
>>
>> result of previous calculation.
>> 141 11.553787
>> 142 11.490255
>> 143 11.434555
>> 144 11.448904
>> 145 11.325060
>> 146 11.329223
>> 147 11.325572
>> 148 11.313778
>> I have the restart file at 140, and start from there, I got the
>> result :
>> 141 11.546061
>> 142 11.599075
>> 143 11.659556
>> 144 11.680797
>> 145 11.647323
>> 146 11.635326
>> 147 11.513223
>> 148 11.503986
>>
>> The second column is a distance of center of mass of 2 groups,
>> and I get this during the Tclforce calculation.
>>
>> They seem to differ quite a lot !! Is this common?
>>
>> Thanks.
>> Bin
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------------
>> The tree of liberty must be refreshed from time to time with the
>> blood of patriots and tyrants.
>>
>
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group Lab: 510.643.2159
> 218 Wellman Hall Fax: 510.642.7428
> University of California, Berkeley http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
> ------------------------------------------------------------------------------------------------------
>
>

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.

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