Re: namd-SMD constant Force missing smdatom location

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Mon Aug 10 2009 - 18:52:06 CDT

> Hi!
>
> On Mon, Aug 10, 2009 at 2:40 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
>
>> Dear NAMD Users,
>>
>> I was following the NAMD-SMD tutorials and found following lines in
>> case of constant force pulling, page 69 of the latest tutorials.
>>
>> "The direction of the force will be specified in the coordinates of the SMD
>> atom.
>> Therefore, you have to write the normal vector in the following way:
>> $smdatom set x nx
>> $smdatom set y ny
>> $smdatom set z nz
>> where nx , ny , and nz have to be replaced by the appropriate values you
>> already
>> calculated above (in our example 0.443, 0.397, and 0.803). Since the VMD
>> OpenGl Display interpretes the numbers just entered as coordinates of the
>> SMD
>> atom, it displays now a inaccurate protein structure. This is OK and
>> we apologize
>> for the poor appearance."
>>
>> Is it possible to do SMD using constant force pulling without VMD? (I
>> think yes!) If yes then where and which file it write down following
>> information?
>>
>> $smdatom set x nx
>> $smdatom set y ny
>> $smdatom set z nz
>>
>> I am unable to find any file where above numbers are written, except
>> in VMD tcl console.
>
>
> You have the answer from the lines you greped from the tutorial:
> "The direction of the force will be specified in the coordinates of the SMD
> atom"
>
> Now, are you saying, you did not find nx ny nz values in the x y z column?!
> Did you write the changes to the reference file (.ref file) ?
> please go through this link (you want to look at #7)
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node18.html
>
> Do hope it helps.
> Ramya
>
>
>>
>> Only information inf force.ref file I can find is:
>>
>> 1. The CA of First residues equal to 1 in B column and
>> 2. CA of Last residue with force in B-column.
>>
>> Any Idea? I will highly appreciate your help.
>>
>> Thank You,
>>
>> S
>>
>>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:18 CST