From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Tue Nov 27 2018 - 16:10:46 CST
Dear Haochuan and Jerome,
Thank you for your response and guidance!
My calculation will not be expensive and I need all all atom coordinates
and some calculate properties by NAMD such as dv in the accelerated MD. I
will check colvars module.
On Mon, Nov 26, 2018 at 7:27 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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?
> 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.
>> 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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