[gmx-users] some question about REMD

[Albert]

Hi Justin:

Thank you very much for eply.

So the modified .mdp file (including the GBSA model setting) is the 
following? Is this correct?

title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; 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
; 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
nstlist = 5 ; 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 = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
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
; 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
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 5
; 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