[gmx-users] How to add calcium ions at desired position?

[Peggy Yao]

Thank all of you for the suggestions!

I then ran the procedures described at
(http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html),
where it adds water before energy minimization, and it also has
position restraint step. But when I came to the step:

grompp -f dyna/pr1_SOLV.mdp -po X_pr1.mdp -c X_em3.gro -r X_em3.gro -t
X_em3.trr -n X.ndx -p X.top -o X_pr1.tpr

mdrun -v -deffnm X_pr1

I got the following error:

-------------------------------------------------------
Program mdrun, VERSION 3.3.2
Source code file: network.c, line: 437

Routine should not have been called:
gmx_sumi
-------------------------------------------------------

I used exactly the same .mdp files as in the tutorial, with the only
modification in pr1.mdp to set T-coupling to "Protein Non-Protein".

Does anybody know what might be the problem? Thanks!

Peggy


On Nov 19, 2007 3:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> Quoting liang <petrucci123 at vip.sina.com>:
>
> > > Never couple solvent and ions separately.  Check out:
> >
> > > http://wiki.gromacs.org/index.php/Thermostats
> >
> > > Try tc-grps = Protein Non-protein
> >
> > excuse me, if the system includes lipid bilayer, how should i set the
> > tc-prgs?
> > Protein + Lipids + Sol and Ion?
> > or Protein + Non-protein ?
>
> I think either would work, but I've personally used protein, lipids, solvent +
> ions.  As long as you're not coupling a very small amount of atoms/ions to its
> own bath then you should avoid problems.
>
> -Justin
>
> >
> > thanks
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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