Re: namd-SMD constant Force missing smdatom location

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Aug 12 2009 - 12:37:30 CDT

Hi all,

I apologize for my ignorance about constant force SMD simulation.
After carefully reading the force.ref file, I found the nx,ny,nz
coordinates. Thank you all for your help.

Regards

S

On Tue, Aug 11, 2009 at 8:53 AM, snoze pa<snoze.pa_at_gmail.com> wrote:
>>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
>
>
> Hi There,
>
>  The changes are already written in .ref file but there is no column
> which specifies smdatom(nx,ny,nz) in any of the the file in SMD
> constant force setup. Only it writes 1 in occ col of first residue and
> K for last residue in beta col. Please look into your file and let us
> know where it writes.
>
> I don't know if I shall use SMDdir command but still it is not
> mentioned in SMD tutorial files using constant force.
>
> I will highly appreciate any help, if someone can suggest me what shall I do?
>
> Thank upoi
>
>
>
>
>
>
>>
>>>
>>> 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
>>>
>>
>>
>

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