Hi, I am trying to calculate the solvation free energy using thermodynamic integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem in getting accurate average temperature . The following is what I did: I found that when doing TI, grompp recommends using 'sd' ( stochastic dynamics ) as integrator ( provides an warning that for decoupled system, it is better to use sd in stead of md ). Also I went through Justin Lemkul's tutorial which also recommends using 'sd' for TI method. So, I tried to use sd integrator.
I wanted to run NVT simulation at 300 K. I also found from manual and also from Justin's website on FEP, sd integrator implicitly controls temperature and so there is no need to specify a thermostat. So, I did not specify any thermostat ( I wrote tcoupl = No ). But, unfortunately, I found that after a long simulation , the average temperature actually goes to 303 K in stead of 300 K( the desired temperature). This happened for all Lambda values where the average temperature turned out to be 303 K. The .mdp file is pasted at the end of the email and I felt I am using reasonable cutoffs and PME as electrostatics. Here is the output from g_energy command to get the temperature. Statistics over 4000001 steps [ 0.0000 thru 8000.0005 ps ], 1 data sets All averages are exact over 4000001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Temperature 303.333 4.78084 4.78082 5.46937e-06 0.043755 Heat Capacity Cv: 12.4764 J/mol K (factor = 0.00024841) I tried three further tests: a) I removed tcoupl = No option . But, it is giving same 303K as average temperature when using sd. a) I tried to specify the Nose-Hoover thermostat along with sd. But still, I found that when using sd, the average temperature is going to 303 K in stead of 300 K. c) Finally, I tried to overlook grompp warning and went ahead and used 'md' along with Nose-Hoover thermostat. This time I found the right average temperature 300 K is being achieved.B But, I understand that for a decoupled system like here, I need to use a method like stochastic dynamics. But , I was wondering why it is reaching 303 K in stead of 300 K when using sd but 300K is achieved when using md. I looked at the mailing list where people had issues with sd and temperature control. But, I could not find a good solution. So, any help on the right protocol will be really appreciated. Here is my .mdp file. ; RUN CONTROL PARAMETERS integrator = sd ; Start time and timestep in ps tinit = 0.0 dt = 0.002 nsteps = 4000000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; OUTPUT CONTROL OPTIONS ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10000 nstvout = 10000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy = 10 ; Output frequency and precision for xtc file nstxtcout = 1000 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.4 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = shift ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-6 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = No ; Groups to couple separately tc_grps = System ; Time constant (ps) and reference temperature (K) tau_t = 1.0 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1 ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; Random seed for Andersen thermostat andersen_seed = 124821 gen-vel = no gen-temp = 300 gen-seed = -1 ; OPTIONS FOR BONDS constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = yes ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Free energy control stuff free-energy = yes init-lambda = .05 delta-lambda = 0 sc-alpha = 0.0 sc-power = 0 sc-sigma = 0.0 couple-moltype = Protein couple-lambda0 = vdw couple-lambda1 = vdw-q couple-intramol = no
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