[gmx-users] Validation of forcefield for small molecules

Hemalatha Jayabal hemalathajayabal at gmail.com
Mon Mar 4 07:24:06 CET 2019

Dear all,
I am working on studying the effect of a molecule on a protein. I am using
CHARMM force-field in GROMACS for a protein (From literature studies and
validation of protein properties, this force field was chosen) and I intend
to study the effect of a molecule on the protein. The molecule taken was
L-Ascorbic acid and I obtained the structure of the file through ZINC
database, CSD and RCSB ligand database (Tried all 3 structures) . I
obtained the topology files for CHARMM using (a) SWISSPDB (b) LigParGen and
(c) ParamChem.org (Gives high penalties , hence I did not use this
topology). In order to validate the force-field of this structure, I took a
box of roughly 2000 molecules (L-Ascorbic acid) and ran a equilibriation,
NVT and NPT (20ns). But, I am unable to obtain the desired density of the
compound (Reported in literature = 1.65 g/cm3) , obtained density from my
MD studies (1.48 g/cm3).

I have tried obtaining charges through semi-empirical DFT and used those
charges as well. But I cannot obtain the density of the compound. This
molecule exists as solid at the given conditions (P= 1 atm, T= 298 K).
Should I look at any other property of the compound? If so, what properties
could be validated for solids?

I am aware that parametrization of a molecule is a tedious process. Should
I go forward and try doing that? Or are there any more parameters or
conditions that I have failed to look at?

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