saving frequency depends on your application. If you would like to capture
short-lived transition, you should reduce the step.
Since you said you did not require much detail, I think your number is
quite reasonable.
You might want to check literature. (e.g ff14SB papers used different
saving frequencies: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255)
Hai
On Mon, Aug 22, 2016 at 9:03 PM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
wrote:
> Dear AMBER users,
>
>
> Just a general question.
>
> As I do not require much details on my protein structure/to reduce file
> size, I am planning to increase the steps written to the output files.
>
> With nstlim = 100,000; dt = 0.001,
>
> I wonder what is the optimum range for NTPR, NTWX and NTWR?
>
> Do you think with NTPR = 5000, NTWX = 2000, NTWR = 5000 is a good choice
> of selection?
>
> As currently, I am setting all the outputs to be generated at every 100
> steps.
>
>
> Thanks in advance.
>
>
> Best regards,
>
> Li Zhe
>
>
> [http://imu.edu.my/e-banner/openday-sep-2016.jpg]
> Interested in joining our September 2016 intake?
> Come visit us at the September Open/Info Days!
> More info at http://ask.imu.edu.my/openday
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 22 2016 - 21:00:03 PDT
