On 11/1/12 12:55 PM, Albert wrote:
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for
16 different temperature with exchange step 300.
Based on your .mdp file, you're not doing NPT (pcoupl = no).
mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s remd_.tpr
-multi 16 -replex 300
I found that it will require 1 months to be finished which is a really long
time.
I am just wondering is there anything I did wrong for the .mdp so that it is so
slow? here is my .mdp file.
One month is not very long, especially if you are running on CPU and not GPU.
How many atoms are in your system? How did you decide that 24 CPU per replica
was appropriate? How did you decide on your exchange frequency? Exchanging
every 0.6 ps sounds awfully frequent, but I'm no REMD expert so I'll leave that
for others to comment on.
-Justin
thank you very much
title = Protein-ligand complex NPT equilibration
; Run parameters
integrator = sd ;
nsteps = 20000000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
nstxout = 0 ; save coordinates every 0.2 ps
nstvout = 0 ; save velocities every 0.2 ps
nstfout = 0
nstxtcout = 500
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
energygrps = Protein_LIG
; Bond parameters
continuation = yes ; first dynamics run
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 = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
rvdw = 0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cutoff ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.15 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_LIG ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 310 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; pressure coupling is on for NPT
; Periodic boundary conditions
; Pressure coupling
pcoupl = no ; pressure coupling is on for NPT
; Periodic boundary conditions
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
pbc=no
; Dispersion correction
DispCorr = no ; account for cut-off vdW scheme
pcoupltype = isotropic ; uniform scaling of box vectors
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
ld_seed=-1
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
comm_mode = ANGULAR
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = 2.25936
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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