Dear All,
In a previous message
(http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html),
I described the results obtained with MD performed with the CHARMM27
ff and the chargegrp "yes" and "no" options of a peptide in TIP3P
water simulated gromacs. Since these results puzzled me a lot, i would
like to share with you others results obtained from the gromacs
community advices to explain these results.
In few words, the context of these simulations. One of my labmate did,
8 months ago (march/april), several simulations of a peptide (25 AA)
with the CHARMM27 ff (and CMAP). The peptide is a transmembrane
segment (TM) and belongs to a large membrane protein. This TM segment
has an initial helical conformation. The simulations were performed in
a cubic box filled with app. 14000 TIP3P water (Jorgensen's model)
with 2 Cl ions. To construct the topology file of the system,
-chargegrp "yes" with pdb2gmx and the MD were done with the gromacs
4.0.5. For some reasons, he had to left the lab, and my boss asked me
to continue his work. When I checked their results, i was very
intrigued by these MD results because he found that the peptide keep
along all the simulation time (100 ns) its initial helical
conformation. This results are not in agreement with circular
dichroism experiments which are shown that the same peptide in water
has no helix segment and is completely unfold. I am aware that the
simulation time is short compared to experiment time scale, however
since i haven't seen any unfolding events in this simulation, so I was
not very confident about these results.
To explain this inconsistency, I have suspected that the error came
probably of the use of the default -chargegrp with CHARMM ff in these
simulations since i have read several recent threads about the charge
groups problems in the CHARMM ff implementation in gromacs. To examine
this hypothesis I have done two simulations with last gromacs version
(4.5.3) and two top files containing charge groups and no charge
groups for the peptide residus. I used the *same* initial pdb file,
box size and simulations parameters. The two simulations were carried
out during 24 ns in the NPT ensemble with the md.mdp parameters
described below after energy minimisation, NVT and NPT equilibration
steps.
constraints = all-bonds
integrator = md
nsteps = 12000000 ; 24000ps ou 24ns
dt = 0.002
nstlist = 10
nstcalcenergy = 10
nstcomm = 10
continuation = no ; Restarting after NPT
vdw-type = cut-off
rvdw = 1.0
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
optimize_fft = yes
nstvout = 50000
nstxout = 50000
nstenergy = 20000
nstlog = 5000 ; update log file every 10 ps
nstxtcout = 1000 ; frequency to write coordinates to xtc
trajectory every 2 ps
Tcoupl = nose-hoover
tc-grps = Protein Non-Protein
tau-t = 0.4 0.4
ref-t = 298 298
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 3.0
compressibility = 4.5e-5
ref_p = 1.0135
gen_vel = no
I found that with charge groups, the peptide remains in its initial
helical conformation, whereas with no charge group, the peptide
unfolds quickly and has a random coil conformation. I have shown these
results to my boss but I was not able to explain why we observe these
differences between the two simulations. Indeed since i use PME in the
MD, chargegroup should not affect the dynamic results (correct ?) . He
asked to do others simulations with different versions of gromacs to
see if is not a bug with charge group implementation in gromacs. For
testing i have done four others MD wit the *same* initial pdb file,
box size and simulations parameters and with previous GMX version
4.5.0 and pre 4.5.2 and with the two types of top files.
In addition since i have done simulations with non optimal parameter
for the vdW et electrostatic, i have also tested the influence of the
vdW et electrostatic MD parameters on the MD by performing two
additional simulations with the parameters used in the Bjelkmar et al
. paper (J. Chem. Theory Comput. 2010, 6, 459–466) (labeled GMX4.5.3
CHARMM in the figures)
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 12000000 ; 2 * 1000000 = 20000 ps
dt = 0.002 ; 2 fs
nstcomm = 10
nstcalcenergy = 10
; Output control
nstxtcout = 1000 ; frequency to write coordinates to xtc
trajectory every 10 ps
nstxout = 50000
nstvout = 50000 ; save velocities every 0.2 ps
nstenergy = 25000 ; save energies every 0.2 ps
nstlog = 5000 ; update log file every 0.2 ps
energygrps = protein Non-Protein
; Bond parameters
continuation = yes ; continuation after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 20 fs
rlist = 1.2
;
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.2
vdw-type = Switch
; cut-off lengths
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
table-extension = 5
fourierspacing = 0.14
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; Temperature coupling is on
tcoupl = nose-hoover ;
tc-grps = protein Non-Protein ; one coupling groups - more
accurate
tau_t = 0.4 0.4 ; time constant, in ps
ref_t = 297 297 ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl = Parrinello-Rahman ; pressure coupling in
NPT
pcoupltype = isotropic
tau_p = 3.0
compressibility = 4.5e-5
ref_p = 1.0135
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
gen_vel = no
The results are presented in the three figures accessibles with the
three links below
http://img4.hostingpics.net/pics/586637ResultatsVSGMX1jpg.jpg ->
Conformation
http://img4.hostingpics.net/pics/392578ResultatsVSGMX2jpg.jpg ->
RMSD vs. time
http://img4.hostingpics.net/pics/271597ResultatsVSGMX3jpg.jpg ->
Secondary structure vs. time
As you can see in all runs with no charge groups option, the peptide
quickly unfolds and have a random coil conformation during the end
of the simulation times, whereas with charge group option, the peptide
remains in its initial (helix) conformation whatever the gromacs
version used.
To finish I saw that in all the simulation seems to be well conserved
CHARGE GROUP 4.5.3 (along the 24 ns of the run)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -561452 5.6 774.891 -1.37923
(kJ/mol)
Total Energy -455901 5.6 959.234 -1.42286
(kJ/mol)
NO_CHARGE GROUP 4.5.3 (along the 24 ns of the run)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -563934 18 774.632 -113.02
(kJ/mol)
Total Energy -458347 18 960.371 -112.951
(kJ/mol)
CHARGE GROUP pre4.5.2 (along the 24 ns of the run)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -562415 5.1 777.12 -33.8615
(kJ/mol)
Total Energy -456864 5.1 964.365 -33.7504
(kJ/mol)
NO_CHARGE_GROUP_PRE_4.5.2
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -564899 4.6 778.002 -3.00182
(kJ/mol)
Total Energy -459312 4.6 963.702 -2.58102
(kJ/mol)
NO_CHARGE_GROUP_PRE_4.5.0
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -563933 30 777.279 -202.641
(kJ/mol)
Total Energy -458346 29 960.748 -202.578
(kJ/mol)
CHARGE_GROUP_PRE_4.5.0
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -561442 8 773.826 -49.7596
(kJ/mol)
Total Energy -455891 8 958.546 -49.7573
(kJ/mol)
USE_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -566048 5.4 765.184 -31.6659
(kJ/mol)
Total Energy -460851 5.4 950.934 -31.7008
(kJ/mol)
USE_NO_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential -568520 24 770.264 -165.498
(kJ/mol)
Total Energy -463287 24 955.755 -165.768
(kJ/mol)
I am particularly eager to obtain from you some comments and advices
about these findings. Thanks you so much for your help.
SA
