Michael Lerner wrote:
Hi,
I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a
CG water box, looking at the diffusion constant of the protein among
other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman
barostat with tc-grps = System. In CHARMM, a protein-in-water simulation
with an extended ensemble will show equal temperatures for the protein
and the water. However, I'm finding that, with ref_t = 323, I get a SOL
(both W and WF particles) temperature of 323 and a Protein temperature
of 295. Is this what I should expect?
The system has 62.5k particles, the box is 20 x 20 x 20, and the
relevant .mdp parameters I've used are:
tcoupl = Nose-Hoover
tc-grps = System
tau_t = 2
ref_t = 323
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 5
compressibility = 5e-5
ref_p = 1.0
These parameters seem to lead to stable systems for bilayer simulations.
I've included the whole .mdp file at the end in case I've forgotten to
mention something relevant.
I calculated temperatures with
g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
I see you are using "constraints = none," but are there any constraints defined
in the topology? If so, as noted in g_traj -h:
"Option -ot plots the temperature of each group, provided velocities are
present in the trajectory file. No corrections are made for constrained
degrees of freedom! This implies -com."
So you will get an inherently incorrect answer when using g_traj, if there are
any constraints.
-Justin
Thanks,
-Michael
------ begin md2.mdp ------
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.020
nsteps = 25500000
; 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 = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 50000
nstvout = 50000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 2500
nstenergy = 2500
; Output frequency and precision for xtc file =
nstxtcout = 2500
xtc_precision = 100
; 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 = System Protein W WF
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 5
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 10
fourier_ny = 10
fourier_nz = 10
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Nose-Hoover
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
tau_t = 2
ref_t = 323
; Pressure coupling =
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5
compressibility = 5e-5
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; GENERATE VELOCITIES FOR STARTUP RUN =
continuation = yes
gen_vel = no
;gen_temp = 323
;gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Relative tolerance of shake =
shake_tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Equal or
Conservative =
disre_weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed = no
disre_fc = 1000
disre_tau = 1.25
; Output frequency for pair distances to energy file =
nstdisreout = 100
------- end md2.mdp -------
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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