From: Sanjib Paul (sanjib88paul_at_gmail.com)
Date: Mon Sep 11 2017 - 01:22:48 CDT
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.
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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