iorga
commented
8 years ago Without noticing the header of this issue (thanks @orbeckst for the detailed description) I did the same modifications to my local install of Gromacs.
- modified the
watermodels.dat:
iorga@p54: > cat /sge/packs/packs_centos/opt/gromacs-5.1.3-openmpi-2.0.0-fftw-auto-centos6-pipin/share/gromacs/top/oplsaa.ff/watermodels.dat
tip4p TIP4P TIP 4-point, recommended
tip4pew TIP4PEW TIP 4-point with Ewald
tip3p TIP3P TIP 3-point
tip3p-m24 TIP3P-M24 TIP 3-point with M24 modification
tip5p TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
tip5pe TIP5P TIP 5-point improved for Ewald sums
spc SPC simple point charge
spce SPC/E extended simple point charge- added the corresponding
tip3p-m24.itpfile, containing the modified atom type
iorga@p54: > cat /sge/packs/packs_centos/opt/gromacs-5.1.3-openmpi-2.0.0-fftw-auto-centos6-pipin/share/gromacs/top/oplsaa.ff/tip3p-m24.itp
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
opls_111 OW 8 9.95140 -0.834 A 3.11100e-01 1.00440e-00
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_111 1 SOL OW 1 -0.834
2 opls_112 1 SOL HW1 1 0.417
3 opls_112 1 SOL HW2 1 0.417
#ifndef FLEXIBLE
[ settles ]
; i j funct length
1 1 0.09572 0.15139
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 628.02 104.52 628.02
#endifHowever, when executing the command gmx pdb2gmx -f spc900.gro -o tip3p-m24-900.gro -p tip3p-m24-900.top -ff oplsaa -water tip3p-m24 I've got the following error:
-------------------------------------------------------
Program: gmx pdb2gmx, VERSION 5.1.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -water
Invalid value: tip3p-m24So it seems that the accepted values of the -water option are not taken from watermodels.dat, but are hard coded. I couldn't find explicitly in the code these values, so probably they are taken from watermodels.dat at the compilation time.
We can conclude that adding a new water model is not easy, it is not generalizable (it needs a specific compilation). I've made a number of trials and the easiest was to temporarily replace the content of tip3p.itp with those of tip3p-m24.itp (but keeping the same name that is recognized by Gromacs). Now the sims with the TIP3P-M24 water model on the dataset92 are running and I will keep you updated with the results.
If this water model gives good results, we might want to use it for our free energy calculations for ligands, but in this case it should be implemented not as a water model, but as a new solvent like octanol and cyclohexane. I know that this is not convenient, but I don't see another solution due to the above-mentioned limitation of Gromacs.
orbeckst
Aim
For testing purposes we should add the M24 water model, introduced by Shirts and Pande1.
Background
Shirts1 introduced a range of proof-of-concept TIP3P-like water models. He changed the epsilon and sigma parameters and obtained much better hydration free energies for amino acid sidechain analogs than with any of the regular models. The one termed M24 performed best. These M* models are not meant for production simulations but are proof-of-concept that fixed charge models and in particular water models still have a lot of room in the parametrization.
M24 water model
Tasks
OPLS-AA force field
Need to add various entries to the bundled force field files
top/oplsaa.ff/m24.itpIn MDPOW
m24to mdpow/forcefields.py — wherevertip3pappears one should also have an equivalentm24entry; note that the corresponding gro file will bespc216.gro.References