[gmx-users] distance between two atoms

V Hariharan vhariharan2.gromacs at gmail.com
Mon Nov 23 18:55:55 CET 2009

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


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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