[gmx-users] Error when performing MD with heavy atoms frozen

[Kai Hu]

Thanks for the fast reply! My system is little bit complicated, it cotains
a protein, an organic ligand plus an iron and several water with 100%
occupancy. I need to simulate this model system to see how these water
interact with ligand and iron. I went through the tutorial Protein with
Ligand, succussfully simulate system with ligand.
Can u tell me how to model in iron and these water? I would like iron and
water oxygens to be frozen at their original positions.
Looking forward to your reply!

-Kai


On Fri, Jun 16, 2017 at 7:19 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/15/17 11:57 AM, Kai Hu wrote:
> > Hi there,
> > I am new to GROMACS, went through Lysozeme in Water tutorial and
> everything
> > runs smoothly.
> > I then tried to immobilize all heavy atoms (except H) in md.mdp file by
> > specifying freezegrps               = Protein-H       ; Freeze all heavy
> > atoms
> > freezedim                = Y Y Y             ; Freeze all dimensions
> > towards the end of the file. I previous generated a index.ndx file using
> > gmx make_ndx command.
> >
> > This time, a fatal error would show up, saying:
> > Fatal error:
> > Bond length not finite.
> >
> > Can anyone tell me briefly what might be wrong that leads to such error?
> > Note, if I remove these two commands in md.mdp file, no error would pop
> up,
> > it seems something must wrong with the freeze commands.
> >
>
> Freezing is an extremely artificial perturbation and if you're applying a
> barostat, you'll get spurious contributions to the virial, as noted in the
> manual.  Application of freezing usually requires corresponding
> energygrp_excl.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Kai Hu

Ph.D. candidate,
Allen's lab, W240-MSC
the Pennsylvania State University
+1-814-777-8651


*"When God closes a door, he always opens a window."*