[gmx-users] Molecule not minimized and NVT failure

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 18 18:07:44 CEST 2016


The number of EM steps doesn't mean anything. The final energy can suggest
that something sensible happened, but the values depend on what your system
has in it. You also should visualize the result of the EM and see if that
fits with your chemical knowledge. PRODRG charges often won't produce
sensible results.


On Mon, Apr 18, 2016 at 6:03 PM suniba <sun.iba2 at gmail.com> wrote:

> Hello users
> I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore,
> following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn
> ligand using chemdraw and minimized the structure using chem3D. However,
> during energy minimization step in gromacs, the values converge earlier
> after 490 steps of minimization. This means that structure is not energy
> minimized properly. Also, during NVT, it crashes very early giving a LINCS
> warning which is posted frequently in mailing list and the 'water' molecule
> not settled error. I have gone through all the solutions and according to
> my knowledge, the problem is with minimization. I am confused now how to
> minimize the structure properly to avoid the error. The long bond warning
> might also arise due to bad minimization? Any suggestions please. If
> require I can paste the ligand co-ordinates.
> With Regards
> Suniba
> Sent from my iPhone
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