Re: How to add a C code to NAMD properly?

From: Faramarz Joodaki (
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.

Best Regards,

On Mon, Nov 26, 2018 at 7:27 AM Jérôme Hénin <> 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?
> Jerome
> On Sun, 25 Nov 2018 at 02:25, yjcoshc <> 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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:22 CST