On 2010-09-14 17.06, Nicolas SAPAY wrote:
Good.
I just calculated tip3p energies for a Charmm tip3p trajectory.
Standard tip3p gives 1.1 kJ/mol per water molecule higher energies.
Thus the LJ on H's gives significant extra attraction which increases the
density.
Great, I obtain a similar result: -40.0 kJ/mol for regular tip3p vs -41.2
kJ/mol for Charmm tip3p (so a difference of 1.2 kJ/mol in favor of Charmm
tip3p).
By the way, I have noted that the SHAKE force constants are different
between Gromacs and Charmm. In the Gromacs implementation, the constant is
376560 kJ/mol/A^2 for the O-H bond and 460,24 kJ/mol/rad^2 for the H-O-H
angle. In the Charmm parameter file, the force constant is 188280
kJ/mol/A^2 for the bond (2 times lower) and 23012 kJ/mol/rad^2 for the
angle (50 times higher). Is there a justification for that?
Charmm (and amber) probably use a different definition of the harmonic
potential. Note that this is not used with constraints, only when you
have flexible models.
Gromacs uses degrees instead of radians in the user input.
Berk
Date: Tue, 14 Sep 2010 15:49:03 +0200
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
From: nicolas.sa...@cermav.cnrs.fr
To: gmx-users@gromacs.org
Hi,
We did some checking.
The value of the density for tip3p reported in the Gromacs Charmm ff
implementation of 1001.7 is incorrect.
This should have been 985.7. The number of 1014.7 for Charmm tip3p is
correct.
I have just done a quick test using dispersion correction
(DispCorr=EnerPres) and the density value extracted from the edr file by
g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
1015.0 +/- 3.6 for Charmm TIP3P.
I would expect that the difference with your number is mainly due to
the
shorter LJ cut-off you are using.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:33:16 +0200
Hi,
I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are different models, so the density
does
not have to be identical.
The Gromacs Charmm FF implementation paper:
http://pubs.acs.org/doi/full/10.1021/ct900549r
gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ
switched
from 1 to 1.2 nm).
I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus
dispersion
correction.
These numbers are quite different. I'll do some checking.
Berk
Date: Tue, 14 Sep 2010 11:00:55 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
On 2010-09-14 10.23, Nicolas SAPAY wrote:
Hello everybody,
I have many difficulties to reproduce TIP3P simulation results with
CHARMM
TIP3P. Regular TIP3P gives systematically a lower density than its
CHARMM
counterpart, independantly from the cutoff for non-bonded
interactions,
the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
Regular 961,067 +/-0,756 g/L
CHARMM 980,860 +/-0,492 g/L
The Enthalpy of vaporization follows a similar scheme:
regular -39,992 +/-0,021 kJ/mol
CHARMM -40,665 +/-0,009 kJ/mol
How about the dispersion correction?
If that is not turned on densities will be too low (in both cases).
In fact, CHARMM gives results closer to what I should obtain at
300K
and 1
bar for TIP3P. I suspect an issue with the bond constraints, but I
can't
locate precisely where it is. Settle parameters are exactly the
same
(as
well as constraints for flexible water). Did someone ever face a
similar
problem?
Rgards,
Nicolas
P.S. I My system is just a box of 1728 water molecules
pre-equilibrated
for 500 ps at 300 K and 1 bar.
P.S. II I'm using the following simulation parameters:
constraints = hbonds
constraint_algorithm = LINCS
continuation = no
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
morse = no
(LINCS or SHAKE should not make any difference since TIP3P is
normally
treated by SETTLE).
Other parameters are:
; COUPLING
; Temperature coupling
tcoupl = Berendsen
nsttcouple = -1
nh-chain-length = 10
tc_grps = System
tau_t = 0.1
ref_t = 300
; Pressure coupling
pcoupl = Berendsen
pcoupltype = isotropic
nstpcouple = -1
tau_p = 1
compressibility = 4.5e-5
ref_p = 1
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.15
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.15
vdwtype = Cutoff
rvdw = 1.0
fourierspacing = 0.10
pme_order = 6
ewald_rtol = 1.0e-6
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 200000
comm_mode = Linear
nstcomm = 1
comm_grps = System
--
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Dept. of Cell& Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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[ Nicolas Sapay - Post-Doctoral Fellow ]
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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