[gmx-users] gmx insert-molecules not inserting molecules

Justin Lemkul jalemkul at vt.edu
Thu Sep 14 01:39:36 CEST 2017

On 9/13/17 5:54 AM, Souparno Adhikary wrote:
> We tried to simulate a small molecule using GROMACS. We generated the
> topology file and the GROMACS coordinate file using the PRODRG server. We
> optimized the molecule prior to generating topology using GAUSSIAN 09.

Don't use PRODRG unless you reparametrize the charges and charge 
groups.  It is well known that the topologies from PRODRG are well below 
the necessary accuracy for an MD simulation.

> However, we tried to study the interaction between multiple copies of the
> same molecule in a water box. We generated the PBC and water box
> successfully and then we went on to using gmx insert-molecules to insert
> multiple copies of the molecule in the waterbox. It yielded the following
> output:
> Reading solute configuration
> Containing 33766 atoms in 11201 residues

You appear to be trying to insert molecules into an already solvated 
system.  There will not be sufficient void space in such a system to add 
anything, so you get zero insertions.  Add your small molecules before 
adding water.


> Reading molecule configuration
> Containing 166 atoms in 1 residues
> Initialising inter-atomic distances...
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>           based on residue and atom names, since they could not be
>           definitively assigned from the information in your input
>           files. These guessed numbers might deviate from the mass
>           and radius of the atom type. Please check the output
>           files if necessary.
> NOTE: From version 5.0 gmx uses the Van der Waals radii
> from the source below. This means the results may be different
> compared to previous GROMACS versions.
> A. Bondi
> van der Waals Volumes and Radii
> J. Phys. Chem. 68 (1964) pp. 441-451
> -------- -------- --- Thank You --- -------- --------
> Try 40
> Added 0 molecules (out of 4 requested)
> Writing generated configuration to g1new.gro
> Output configuration contains 33766 atoms in 11201 residues
> What could be the possible problem??? We used the gmx insert-molecules as:
> gmx insert-molecules -f mol1wt.gro -ci mol1_op.gro -o mol1new.gro -nmol 4
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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