Re: a question about modifying the NAMD input file

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 25 2010 - 12:56:36 CDT

On Mon, Oct 25, 2010 at 1:06 PM, ying yu <helen.yingyu_at_gmail.com> wrote:
> Hi,
>
> I am running the NAMD with the attached input file, but it comes with the
> error::
>
>  ------------- Processor 0 Exiting: Called CmiAbort ------------
>
> Reason: FATAL ERROR: number of steps must be a multiple of stepsPerCycle
>
>     while executing
>
> "run $propsteps"
>
>     (file "revized_siliconmechanicstest.namd" line 121)
>
>
>
> Fatal error on PE 0> FATAL ERROR: number of steps must be a multiple of
> stepsPerCycle

well, this error message should be pretty self-explanatory.

>     while executing
>
> "run $propsteps"
>
>     (file "revized_siliconmechanicstest.namd" line 121)
>
> I modified the input file:
>
> "Set propsteps 54000 (was 48000)"

>  There is no error comes out, the running result is as following:

exactly. since 54000 is divisible by 18 and 48000 is not.

> WallClock: 27273.595703  CPUTime: 27268.335938  Memory: 130.688446 MB

>
>
> I am new to NAMD, I am not sure whether I did the right thing, and the
> results make sense? Thanks

the line above is not the result, it only tells you how fast or slow
that specific run was and how much memory it has consumed.

the trajectory that is produced in between is the real result
and whether that is meaningful or not is not that easy to say.
54000 steps if for certain not a lot (~100ps).

the input file that you have attached seems _very_ aggressive
and particularly turns off long-range electrostatics. that will have
a significant impact on the accuracy of the results. you can look
up details in some standard text books on molecular dynamics
(of bio-systems).

cheers,
    axel.

> Helen
>
>
>
>
>
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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