From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 26 2018 - 06:27:24 CST
To add to Haochuan's remark: the best way to do it will vastly depend on
what you are calculating, and what it depends on: positions? velocities?
forces? few atoms, many atoms, all atoms? box size? pressure? Is it an
expensive calculation? Do you need to parallelize it?
Jerome
On Sun, 25 Nov 2018 at 02:25, yjcoshc <yjcoshc_at_gmail.com> wrote:
> Hi Faramarz,
>
> If you only require the atomic coordinates and the current step, you can
> utilize the colvars module. The usage can be found in the NAMD manual.
>
> Regards,
>
> Haochuan Chen
>
>
> 在 2018/11/24 上午2:58, Faramarz Joodaki 写道:
> > Hi everyone!
> >
> > I would like to do some calculations on trajectory for each step of a
> > MD simulation. It is a long MD simulation so saving all steps in dcd
> > file is impossible.
> > Hence, I need to add some codes to the source code of NAMD to
> > calculate some properties during MD simulations (Runtime). I was
> > wondering if there is a proper way to do that. Actually, I can go
> > inside the source code and change or add my C code but I am looking
> > for an efficient way to do that such as linking my code to the source
> > code of NAMD. I would be so grateful if you could guide me with this
> > matter.
> >
> > Best Regards,
> > Faramarz
>
>
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