[gmx-users] How to modify or avoid some molecule clashing with another ?

Chih-Ying Lin chihying2008 at gmail.com
Thu Dec 31 01:57:27 CET 2009

After reading the log file and watching the trajectory movies(nstxout = 1),
some molecule clashes with another in my simulation system.

How can i avoid the situation happening again?
How to modify the broken simulation?

Thank you

Message: 4
Date: Wed, 30 Dec 2009 19:00:51 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] some molecule clashing with another ?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B3BE9B3.8020100 at vt.edu>
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Chih-Ying Lin wrote:
> Hi
> My simulation broke down and the simulation procedues are as follows.
> 1. center a protein molecule in the simulation box
> 2. put 20 ligands around the protein with  " genbox " command
> 3. make sure that any atom of the ligands does not overlap on any atom
> of the protein with Visulization-software.
> 4. solvent addition , with the command " genbox *-vdwd*  0.2   "
> 5. Addition of ions, with the command " genion "
> 6. Energy minimization of the solvated system
> 7. Position restrained MD
> => simulation broke down.
> => It is very probable that some molecule clashing with another.
You can change "probable" to an actual answer if you analyze whatever LINCS
warnings are occurring (the atoms are listed) and by watching the resulting
> => since i have made sured that any atom of the ligands does not overlap
> on any atom of the protein with Visulization-software,
>       the clashed pair of the molecules are possible " solvent vs
> solvent "    or     "solvent vs protein"       or       "solvent vs
> ligand "
Then you should follow up #4 above with another visual inspection, as you
with protein-ligand interactions, in addition to any information printed to
log file (as above).
> => however, from the Gromacs manual , command "genbox"
>      " Solvent molecules are removed from the box where the distance
> between any atom of the solute molecule(s) and any atom of the solvent
> molecule is less
>      than the sum of the VanderWaals radii of both atoms. A database
> (vdwradii.dat <http://manual.gromacs.org/current/online/dat.html>) of
> VanderWaals radii is read by the program, atoms not in the
>      database are assigned a default distance -vdw."
So solvent-solvent overlap shouldn't be a problem.
> =>  here is    vdwradii.dat  (the ligand is simply made of C, N, O, H)
Yes, this is standard.
> ; Very approximate VanderWaals radii
> ; only used for drawing atoms as balls or for calculating atomic overlap.
> ; longest matches are used
> ; '???' or '*' matches any residue name
> ; 'AAA' matches any protein residue name
> ???  C     0.15
> ???  F     0.12
> ???  H     0.04
> ???  N     0.110
> ???  O     0.105
> ???  S     0.16
> My questions are
> 1. anything wrong of my simulation procedures ?
In theory, not really.  What values of potential energy and maximum force
the energy minimization converge to?
> 2. how to find the clashed molecules ?
Read the information printed to the log file (again, I'm assuming you're
LINCS warnings, but you haven't told us what "broke" means!) and watch the
trajectory to see where things start to fall apart.  As I suggested to
earlier, if the crash is happening reasonably early, setting "nstxout = 1"
is a
useful diagnostic to capture all frames prior to the crash.
> Thank you
> Lin
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu |               (540) 231-9080         (540) 231-9080
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