[Pragati Sharma]

Hey Users,

I am running a coarse grained simulation of 10mer PB. After 10 steps, each of 2 ns, the non-bonded potentials seem to converge But the bonded interactions are smoothed but seem a little shifted (attached files). The convergence limit ( as seen from AB.bond.conv) also does not change in these 10 steps (equal to ~ 100)  and  (I don't think It will match anymore)

The convergence limit I have given is 0.003.

Should the simulation be stopped at this point. I am confused if my bonded potentials are correct?

Thanks

[Christoph Junghans]

There are scaling factors for the conversion factor you can set for
each interaction, that is is useful if one interaction hasn't fully
converged yet, like in your case.

To your question, I would run it a little longer, e.g. you could just
iterate the bonded interaction for 50 steps overnight and see where it
gets. you

Christoph

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Christoph Junghans
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[Pragati Sharma]

Thanks christoph for the prompt response. 

I have one query though.

I am running csg_inverse and consequent mdrun command for all steps using run.sh script. I want to run the command in background.

I tried  writing "nohup" with mdrun in settings.xml file. Also tried adding nohup before csg_inverse in script or also from the terminal. But the process does not go to background and stops as soon shell is closed.

How can I run the run.sh in background.

Thanks for your help.

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[Christoph Junghans]

On Wed, Aug 26, 2020 at 10:53 AM Pragati Sharma <praga...@gmail.com> wrote:
>
> Thanks christoph for the prompt response.
>
> I have one query though.
>
> I am running csg_inverse and consequent mdrun command for all steps using run.sh script. I want to run the command in background.
> I tried writing "nohup" with mdrun in settings.xml file. Also tried adding nohup before csg_inverse in script or also from the terminal. But the process does not go to background and stops as soon shell is closed.
> How can I run the run.sh in background.

I think "nohup run.sh &" should work.

Christoph

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[Pragati Sharma]

The command  "nohup run.sh &"  does not work for running run.sh in background.

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[Christoph Junghans]

On Thu, Aug 27, 2020, 01:16 Pragati Sharma <praga...@gmail.com> wrote:

The command  "nohup run.sh &"  does not work for running run.sh in background.

What is the error message?

Otherwise try running it normally in foreground and then press control-Z and type 'bg' (see https://www.informit.com/articles/article.aspx?p=2854374&seqNum=6)

Christoph

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[Jens Wehner]

`disown` might be the solution.