Re: Run-time system modification

From: Jérôme Hénin (
Date: Mon Nov 29 2010 - 06:26:47 CST

Hi Josh,

On 29 November 2010 00:40, JC S <> wrote:
> Hi Jérôme,
> Thank you for responding. Sorry, I am an undergrad and new at this.
> I'll try to be more clear. I need to be able to have my program look
> at atom locations at specific time-steps. Then based on its analysis,
> it needs to be able to move certain atoms before the simulation
> continues.

That could be tricky. It is fairly easy to modify a NAMD simulation by
applying external forces, but the algorithm is really not designed to
have atoms moving around outside its control. That is likely to
require stopping and restarting the simulation each time, as mentioned
in this thread:

The bottom line is that you might be better off looking for another MD
engine, less effective but simpler and more flexible. It also depends
on the size of your model, what hardware you have access to, and your
throughput requirements.

> Also, how would I add this email to the correct namd thread? Should I
> just add to recipients with the "Re:" in the title,
> should I remove the "Re:"?

I have added the list back as a CC. Normally, just hitting "reply to
all" works fine.

> On Tue, Nov 23, 2010 at 3:05 AM, Jérôme Hénin <> wrote:
>> Hi Josh,
>> Anything is possible, if you are willing to rewrite the relevant parts
>> of NAMD. That's the power of open-source.
>> Depending on what exactly you want to do, there may be much easier
>> ways, but then you need to be more specific about what you are trying
>> to achieve. By "applying empirical constants", do you mean
>> constraints? If so, what kind of constraints?
>> Cheers,
>> Jerome
>> On 23 November 2010 06:38, JC S <> wrote:
>>> Hi,
>>> Is it possible to modify a namd simulation run after every time-step
>>> with my own program? I need to apply empirical constants on the system
>>> that cannot be simulated due to time. Any information on this would be
>>> helpful.
>>> Thanks,
>>> Josh

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