Re: firsttimestep question

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Mon Oct 06 2008 - 13:00:08 CDT

Sure, here's an example:

Say, in my 1st namd job config file:

set inpname hc_eq_4
set outname free_eq
firsttimestep 0

and the 1st job is stopped after running for 47000 time steps. So, to
resume the job, I usually set up the 2nd job config file as:

set inpname free_eq
set outname free_eq2
firsttimestep 47000

My question is, for the 2nd job config file, can I set firsttimestep to "0"?

set inpname free_eq
set outname free_eq2
firsttimestep 0

And then add the 47000 offset to get the correct time steps in the 2nd
run? Would that affect any physical parameters calculated by namd?

Thanks!

-Dong Xu

On Mon, Oct 6, 2008 at 5:32 AM, Chris Harrison <charris5_at_gmail.com> wrote:
> Dong Xu,
>
> It is not entirely clear what you mean by "calculate the correct timestep
> later by adding the last time step of the previous run." Can you provide an
> example of what you want to do?
>
> -Chris
>
>
>
> On Mon, Oct 6, 2008 at 12:00 AM, Dong Xu <d1xu_at_ucsd.edu> wrote:
>>
>> Hi,
>>
>> When a namd free equilibration job is resumed, we usually change
>> firsttimestep to the last time step of a previous run.
>>
>> My question is: is it ok setting it to 1 and calculate the correct
>> timestep later by adding the last time step of the previous run?
>> Setting firsttimestep shouldn't affect any other physical parameters
>> of the simulation such as energies etc. Correct?
>>
>> Thanks a lot in advance,
>>
>> -DX
>>
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>

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