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

From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Wed Dec 05 2018 - 18:39:07 CST

Dear Haochuan,

Thank you again for your guidance and sorry for my late response!

Yes, NAMD can save dv evey step. I think for this parameter, I am going to
save them and then apply my calculation on them.

I have a question about colvars module. If covalrs module have an access to
all coordinated of atoms, how can I apply my calculation on them?

Best Regards,
Faramarz

On Tue, Nov 27, 2018 at 8:44 PM yjcoshc <yjcoshc_at_gmail.com> wrote:

> Hello Faramarz,
>
> As far as I know, the aMD's dV is not collected to the colvars module.
> Maybe you want to use your own histogram code and the dV to reweight the
> trajectory on the fly. Actually I have tried to modify the NAMD's code to
> make it working with the histogram in colvars:
>
> 1. Export dV from NAMD's TCL interface and implement a getaMDWeight TCL
> command to get the dV in the NAMD configuration file every step;
>
> 2. Modify the histogram bias in colvars to make it accept the weight on
> the fly (the weight can be set by calling cv bias histo1 reweight w);
>
> 3. Modify the NAMD configuration accordingly.
>
> In this way I have to set stepspercycle to 1 and use a TCL loop with "run
> 1" to reweight the histogram on the fly, so it's rather slow.
>
> A faster way may be to collect the dV to colvars module through the C++
> interface (NAMD's GlobalMaster) directly. The NAMD's code, however, are
> rather undocumented and currently I don't work on it.
>
> If you have some better ideas please let me know.
>
> Thanks,
>
> Haochuan Chen
>
>
> 在 2018/11/28 上午6:10, Faramarz Joodaki 写道:
>
> 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,
> Faramarz
>
> 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?
>>
>> 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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