Dear Pooja,
2016-09-15 17:18 GMT+02:00 Pooja Kesari <pkesari88.gmail.com>:
> Dear All,
> I am new to this amber. So I have some basic questions.
> Initially, I had some amber files which ran successfully for 4 ns. Now I
> want to continue the same run from 4ns till 10ns.
> Question 1. Is it worth to continue the run and does it work in the same
> way ?
>
It depends upon the question you want to address. I guess you will find
interesting discussion in amber archive on this issue. It's always worthful
to extend MD in cases where longer simulation time scale is required.
> Question 2. If in case I have to continue the run , How can I do so?
>
You can continue run by reading the .rst file
of
the previous
MD run
. Following is the input for it
*sander*
* -O -i Data_03.in -o Data_03.out -p rec_solvated.top -c Data_02.rst -r
Data_03.rst -x Data_03.mdcrd*
> Question 3. How to monitor the time production run will take once for 10 ns
> run to finish?
>
mdinfo file is written with this information.
> Question 4. Can I analyse the production run files in between; will it not
> disturb the on-going run ?
>
It's absolutely ok to read and analyse the production run files. Though,
It's better to break up the production run into short (eg 2 ns)
run.
Regards,
>
>
>
>
>
> --
> Thanks & Regards,
> Pooja Kesari
> Research Scholar
> Department Of Biotechnology
> Indian Institute of Technology Roorkee
> INDIA
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>
--
*Bilal Nizami*
School of Health Sciences
University of KwaZulu-Natal
Durban
4000
South Africa
Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
Email: 214573074.stu.ukzn.ac.za
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Received on Thu Sep 15 2016 - 10:30:03 PDT
