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
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