Dear All, <br><br>In a previous message (<a href="http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html">http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html</a>), 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. <br>
<br>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.<br>
<br>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. <br>
<br>constraints = all-bonds<br>integrator = md<br>nsteps = 12000000 ; 24000ps ou 24ns<br>dt = 0.002<br><br>nstlist = 10<br>nstcalcenergy = 10<br>nstcomm = 10<br><br>continuation = no ; Restarting after NPT<br>
vdw-type = cut-off<br>rvdw = 1.0<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-05<br>optimize_fft = yes<br><br>nstvout = 50000<br>nstxout = 50000<br>
nstenergy = 20000<br>nstlog = 5000 ; update log file every 10 ps<br>nstxtcout = 1000 ; frequency to write coordinates to xtc trajectory every 2 ps<br><br>Tcoupl = nose-hoover<br>
tc-grps = Protein Non-Protein<br>tau-t = 0.4 0.4<br>ref-t = 298 298<br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 3.0<br>
compressibility = 4.5e-5<br>ref_p = 1.0135<br>gen_vel = no<br><br>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. <br>
<br>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) <br>
<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 12000000 ; 2 * 1000000 = 20000 ps<br>dt = 0.002 ; 2 fs<br>nstcomm = 10<br>nstcalcenergy = 10<br>
; Output control<br>nstxtcout = 1000 ; frequency to write coordinates to xtc trajectory every 10 ps<br>nstxout = 50000<br>nstvout = 50000 ; save velocities every 0.2 ps<br>nstenergy = 25000 ; save energies every 0.2 ps<br>
nstlog = 5000 ; update log file every 0.2 ps<br>energygrps = protein Non-Protein<br>; Bond parameters<br>continuation = yes ; continuation after NVT<br>constraint_algorithm = lincs ; holonomic constraints<br>
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>
ns_type = grid ; search neighboring grid cels<br>nstlist = 10 ; 20 fs<br>rlist = 1.2<br>;<br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.2<br>
vdw-type = Switch<br>; cut-off lengths <br>rvdw-switch = 1.0<br>rvdw = 1.2<br>DispCorr = EnerPres<br>table-extension = 5<br>fourierspacing = 0.14<br>
fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>
optimize_fft = no<br>; Temperature coupling is on<br>tcoupl = nose-hoover ;<br>tc-grps = protein Non-Protein ; one coupling groups - more accurate<br>tau_t = 0.4 0.4 ; time constant, in ps<br>
ref_t = 297 297 ; reference temperature, one for each group, in K<br>; Pressure coupling is off<br>pcoupl = Parrinello-Rahman ; pressure coupling in NPT<br>pcoupltype = isotropic<br>
tau_p = 3.0<br>compressibility = 4.5e-5<br>ref_p = 1.0135<br><br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>gen_vel = no<br><br>The results are presented in the three figures accessibles with the three links below<br>
<br><a href="http://img4.hostingpics.net/pics/586637ResultatsVSGMX1jpg.jpg">http://img4.hostingpics.net/pics/586637ResultatsVSGMX1jpg.jpg</a> -> Conformation<br><a href="http://img4.hostingpics.net/pics/392578ResultatsVSGMX2jpg.jpg">http://img4.hostingpics.net/pics/392578ResultatsVSGMX2jpg.jpg</a> -> RMSD vs. time<br>
<a href="http://img4.hostingpics.net/pics/271597ResultatsVSGMX3jpg.jpg">http://img4.hostingpics.net/pics/271597ResultatsVSGMX3jpg.jpg</a> -> Secondary structure vs. time<br><br>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.<br>
<br>To finish I saw that in all the simulation seems to be well conserved<br><br>CHARGE GROUP 4.5.3 (along the 24 ns of the run) <br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
Potential -561452 5.6 774.891 -1.37923 (kJ/mol)<br>Total Energy -455901 5.6 959.234 -1.42286 (kJ/mol)<br><br>NO_CHARGE GROUP 4.5.3 (along the 24 ns of the run) <br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential -563934 18 774.632 -113.02 (kJ/mol)<br>
Total Energy -458347 18 960.371 -112.951 (kJ/mol)<br><br>CHARGE GROUP pre4.5.2 (along the 24 ns of the run) <br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
Potential -562415 5.1 777.12 -33.8615 (kJ/mol)<br>Total Energy -456864 5.1 964.365 -33.7504 (kJ/mol)<br><br>NO_CHARGE_GROUP_PRE_4.5.2<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Potential -564899 4.6 778.002 -3.00182 (kJ/mol)<br>Total Energy -459312 4.6 963.702 -2.58102 (kJ/mol)<br>
<br>NO_CHARGE_GROUP_PRE_4.5.0<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential -563933 30 777.279 -202.641 (kJ/mol)<br>
Total Energy -458346 29 960.748 -202.578 (kJ/mol)<br><br>CHARGE_GROUP_PRE_4.5.0<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
Potential -561442 8 773.826 -49.7596 (kJ/mol)<br>Total Energy -455891 8 958.546 -49.7573 (kJ/mol)<br><br>USE_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings <br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential -566048 5.4 765.184 -31.6659 (kJ/mol)<br>
Total Energy -460851 5.4 950.934 -31.7008 (kJ/mol)<br><br>USE_NO_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings <br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Potential -568520 24 770.264 -165.498 (kJ/mol)<br>Total Energy -463287 24 955.755 -165.768 (kJ/mol)<br>
<br>I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. <br><br>SA<br>