Re: namd-SMD constant Force missing smdatom location

From: snoze pa (
Date: Tue Aug 11 2009 - 08:53:46 CDT

>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)
> 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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