From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Sep 11 2017 - 05:12:50 CDT
TclBC looks like what you need.
On 11 September 2017 at 08:22, Sanjib Paul <sanjib88paul_at_gmail.com> wrote:
> I have followed NAMD manual. But did not get any fruitful idea.
> What I have come to know from tutorial and manual is that center of mass of
> SMD atoms move along the direction determined by SMD and fixed atoms. But
> in my problem, I want to apply force on each and every water molecule along
> +z or -z direction. The atoms belong to carbon nanotube are fixed. Any
> suggestion to solve this problem will be really very helpful to me.
> Thanking you.
> Sanjib Paul
> Department of Chemistry
> Indian Institute of Technology, Kharagpur
> On Wed, Sep 6, 2017 at 5:38 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> Only a few basic features are covered in the NAMD *tutorial*.
>> You want to choose one of many options to apply external, user-defined
>> forces, all of which are covered extensively in the NAMD *manual*:
>> On Wed, Sep 6, 2017 at 7:14 AM, Sanjib Paul <sanjib88paul_at_gmail.com>
>>> Dear Namd users,
>>> I have a system where two water baths are
>>> connected through a single walled carbon nanotube. I want to apply a
>>> constant force on all water molecules of these two baths along a particular
>>> direction (say +z or -z direction). The water molecules inside the nanotube
>>> will not experience any external force. Few research groups have done these
>>> type of simulation using steered molecular
>>> dynamics (Zhu *et al*. Biophysical Journal, *83*, *2002*, 154 –160). I
>>> have gone through the NAMD tutorial but what I am trying to do is quite
>>> different from the content kept in tutorial. So can anyone please show me a
>>> way to do this?
>>> Thanking you.
>>> Sanjib Paul
>>> Department of Chemistry
>>> Indian Institute of Technology, Kharagpur
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
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