Hi Justin, I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the following change:
gen-vel = yes gen-temp = 280 gen-seed = -1 So, essentially, I heated the minimized system up from 280 K with ref_t 300K using sd integrator. But, here also I found the average temperature goes to 303 K( instead of 300 K) . One thing I don't understand that why using md as integrator gives the desired average temperature( when using Nose-Hoover thermostat) while the sd integrator does not. Any further suggestion will be appreciated. Jagannath ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tue, August 2, 2011 8:08:20 PM Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP Sanku M wrote: > 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. > The tutorial uses BAR for calculation free energy, not TI. Though the protocols are similar, there is a difference, FYI. > 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. > >From the manual description of the sd integrator: "The parameter tcoupl is ignored." This explains (a) and (b). > 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. > What type of equilibration did you do prior to the data collection? If your system isn't sampling the desired ensemble, then you shouldn't proceed. -Justin > > 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 > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
