[gmx-users] Water model properties

Harshkumar Singh harshsingh2293 at gmail.com
Mon May 26 05:03:05 CEST 2014

I'm using version 4.5.4 and very new to this software.
Trying to follow this paper-

* A systematic study of water models for molecular simulation: Derivationof
water models optimized for use with a reaction field David van der Spoel,a)
Paul J. van Maaren, and Herman J. C. Berendsenb)*

1.It says to use the SETTLE algorithm for constraining bonds but I can only
get the options of using Lincs or Shake otherwise it shows an error.

2.I went ahead using the Lincs algorithm but many of the properties do not
give the same results.How do I resolve that?

My steps were
1.converting the pdb file and then using editconf for making the box.
2.used grompp as the same it was in the tutotials with the changes made
accordingly in the .mdp file according to the paper.
3.then the analysis with g_dipoles and g_energy.
4.only dipole moment was correct and rest other properties like
epsilon,kirkwood factors,potential energy,density,temperature,pressure
showed too much deviation.
Harshkumar Singh
2nd Year Integrated MSc Chemistry
IIT Bombay.

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