[gmx-users] Using restrained positions

Jon jon.ellis at utoronto.ca
Fri Aug 12 16:41:00 CEST 2005


> Message: 4
> Date: Thu, 11 Aug 2005 19:51:51 -0400
> From: Bob Johnson <robertjo at physics.upenn.edu>
> Subject: 		
> To: GROMACS Mailing List <gmx-users at gromacs.org>
> 
> Hello everyone,
> I'm currently studying the interaction between single stranded DNA and a carbon
> nanotube. Because the DNA seems to distort the nanotube, I'm trying to restrain
> the positions of the carbon atoms in a nanotube. However, I'm having problems
> with this step as I'm not sure how to implement the posre.itp file.

...

> 
> [ position_restraints]
> ;atom           type            fx        fy        fz
>       1          1              1e9       1e9       1e9
>       2          1              1e9       1e9       1e9
>       3          1              1e9       1e9       1e9
>       4          1              1e9       1e9       1e9
>       5          1              1e9       1e9       1e9
> ..
> 
> This posre_nanotube.itp file lists atoms 1-2080 as the atoms that are to be
> restrained (note that these are the nanotube atoms as listed in the .g96 file).
> I add the keyword -DPOSRES_NANOTUBE to the input file and placed the necessary
> include statements in the nanotube topology file. However, I get the
> following error upon execution of grompp.
> WARNING 1 [file "posre_nanotube.itp", line 5]:
>   No default Position Rest. types for perturbed atoms, using normal values
> WARNING 2 [file "posre_nanotube.itp", line 6]:
>   No default Position Rest. types for perturbed atoms, using normal values

I got this problem a little while ago as well, and I resolved it by 
putting the posres force values twice for each atom, ie

 > [ position_restraints]
 > ;atom      type      fx        fy        fz
 >       1     1        1e9       1e9       1e9   1e9       1e9 
1e9
 >       2     1        1e9       1e9       1e9   1e9       1e9       1e9
 >       3     1        1e9       1e9       1e9   1e9       1e9       1e9
...

You have to get the column spacing right, of course.

Don't know why it worked, but David suggested it on the mailing-list a 
while ago. Is it a glitch in the posres procedures?

Cheers
Jon

----------
Jon Ellis
PhD Candidate, Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto





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