[gmx-users] distance between two atoms

[V Hariharan]

Search the manual about freezing groups. I think the command is freezegrps.
This will fix the atoms in space.

--Venk

On Sun, Nov 22, 2009 at 7:25 AM, udi <udi_zel at 012.net.il> wrote:

>  Hello all Gromacs users,
>
> I’m simulating a 255 a.a peptide which is only a segment of a whole
> protein.
>
> I’m using the triclinic box with  -d 1.2 nm.
>
> Because the peptide is only a segment out of a larger protein I would like
> to restrain the ends of the peptide in order to prevent the peptide
>
> from closing on its self during the simulation.
>
> I thought to apply distance restraint in order to do so.
>
> Using VMD I measured the distance between the C-alphas of the first and
> last a.a. of the peptide and got 88.8A.
>
> I wanted to double check the distance, so I used g_dist and g_mindist and
> got a 56A!!!
>
> I guess that PBC is the reason for the difference.
>
> Which distance (VMD or Gromacs) should I use when applying the distance
> restraint?
>
> Is  such a distance restrain (88.8A) even possible? (too long?)
>
> I would be glad to learn any other way to enforce a minimal movement of
>  the ends of the peptide.
>
> Thanks in advance,
>
> Udi
>
>
>
>
>
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-- 
__________________________________
Venkatesh Hariharan
Columbia University | Biomedical Engineering
Graduate Research Assistant

"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi
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