Carla Jamous wrote:
Hi,
what do you mean: "use gmxdump to trace the molecule"?
I'm a beginner with gromacs and all I found about gmxdump is that it
reads a binary file & prints that to standard output in a readable format.
So how can I check if my atom number is the same in my pdb file & my
output file?
Carla
On Wed, Sep 30, 2009 at 4:38 AM, Itamar Kass <[email protected]
<mailto:[email protected]>> wrote:
Hi,
another point you should consider is that the atom/molecule number
in the pdb or gro file are not necessarally the what you see in your
output. You should use gmxdump in such cases to trace the molecule.
Hmm? Why would the atom numbers not be accurate? Perhaps they might be
out by one if there's a counting-from-zero vs counting-from-one
mismatch, but surely nothing worse than that... And how would gmxdump help?
Mark
"In theory, there is no difference between theory and practice.
But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
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|
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On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <[email protected]
<mailto:[email protected]>> wrote:
2009/9/29 Justin A. Lemkul <[email protected]
<mailto:[email protected]>>
Carla Jamous wrote:
Thank you for your reply,
but none of the water molecules with error messages is
trapped inside my protein, nor is it in contact with the
protein or the ions in my system.
Also if the water molecules are positioned properly, you can try
define = -DPOSRES_WATER in your .mdp file with a high value set
in your topology(.top) file under [position restraint] section as,
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
#endif
-Manik
Then you need to watch the trajectory and see where things
go wrong. In unstable systems, I often set "nstxout = 1" to
capture as many frames in the .trr file as possible (if the
crash is happening early, as it is in your case).
Likely, energy minimization did not resolve all the bad
contacts, but may still have converged within your criteria.
You could also specify a lower target Fmax during EM to see
if things resolve.
-Justin
Carla
On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
wrote:
Hi Carla,
You may have a water molecule trapped inside your
protein. Check the
water molecule with the given atom number in a
viewer, together with
your structure. If it is inside, you can try to
remove it manually
from the system, editing the structure file and
decreasing the amount
of solvent listed in te topology file. If you edit
the .gro file, do
mind to decrease the number on the second line (the
number of atoms)
by three.
Hope it helps,
Tsjerk
On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
> Hi,
> I have a problem with water molecules in my
system: I'm using
Gromacs with
> ffamber94 force-field. During minimization, I have
this message:
>
> t = 0.014 ps: Water molecule starting at atom
10045 can not be
settled.
> Check for bad contacts and/or reduce the
timestep.Wrote pdb files
with
> previous and current coordinates
>
> The minimization converged. However, molecular
dynamics were stopped.
> I tried minimization with different parameters:
Flexible,
> position-restrained, reducing my timestep, etc...
and nothing worked.
>
> I also tried one simulation with TIP3P water model
and another
simulation
> with SPC water model and I still get the same error.
> I tried to access: oldwiki.gromacs.org
<http://oldwiki.gromacs.org>
<http://oldwiki.gromacs.org> but access is denied.
>
> Please does anyone have a solution to propose?
>
> Thanks
> Carla
>
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Biomolecular NMR, Bijvoet Center
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Department of Biochemistry
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jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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