Hi Justin:
thank you so much for such kind and helpful comments. My system is a
protein/ligand system.
I will try it with your advices these days.
best
Albert
On 10/17/2012 07:58 PM, Justin Lemkul wrote:
On 10/17/12 1:52 PM, Albert wrote:
Hi Justin:
Thank you very much for eply.
So the modified .mdp file (including the GBSA model setting) is the
following?
Is this correct?
No. See inline comments.
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
There is no need for restraints. There is no solvent to equilibrate
around the protein.
; Run parameters
integrator = sd ;
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
energygrps = Protein JZ4
This is only appropriate if you're following the tutorial exactly.
From your previous description, you are dealing with a protein and no
ligand.
; Bond parameters
continuation = no ; 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 = grid ; search neighboring grid cells
You need ns-type = simple.
nstlist = 5 ; 10 fs
Set nstlist = 0 for a fixed neighbor list. In conjunction with
infinite cutoffs, you will use the all-vs-all kernels, which are
highly optimized.
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 = PME ; Particle Mesh Ewald for long-range electrostatics
Set coulombtype = cutoff.
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
Note that tcoupl is ignored when using the sd integrator.
tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more
accurate
You don't have water and ions in an implicit system, and likely you
don't have a ligand.
tau_t = 0.1 0.1 ; time constant, in ps
tau_t is too low for sd, use something like 1.0.
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc=no
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
Unnecessary with infinite cutoffs.
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = yes
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
This should also be set to zero.
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 5
Set to zero.
-Justin
; 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 = -1
On 10/17/2012 07:45 PM, Justin Lemkul wrote:
On 10/17/12 1:43 PM, Albert wrote:
hello Justin:
thanks a lot for kind reply.
I've got another question: how to disable PBC? shall I simply
delete "pbc=xyz"
from .mdp file? I found that sometimes if we delete some parameters
from .mdp,
gromacs will use the default instead of disable it.
The default setting for pbc is xyz, so deleting the line
accomplishes nothing.
Set "pbc = no" in the .mdp file.
-Justin
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