[gmx-users] In-Vacuo ligand only equilibration

[Iris Nira Smith]

Hello, 

I'm utilizing gromacs 4.6.3 to set up my md simulation to run a ligand-only invacuo (no water) system for 500 ps prior to running my protein-ligand complex to determine the stability of the ligand. I have successfully run an energy minimization with the em-invaco.mdp file below (in absence of periodicity and infinite cut-offs). 

When running the equilibration should it be broken up into 2 phases: phase 1-nvt, phase 2-npt or is nvt sufficient? 
If so, should it also be done utilizing an implicit solvent model such as GBSA for both equilibration and production run (see also eqb-invacuo.mdp below)? 



em-invacuo.mdp 
; Parameters describing what to do, when to stop and what to save 
integrator = steep ; Algorithm options 
; steep = steepest descent minimization 
; MD = Leap Frog algorith for integrating Newtonś equations of motion ) 
emtol = 10.0 ; Stop minimization when the Fmax < 10 kJ/mol/nm. 
emstep = 0.01 ; Energy step size 
nsteps = 10000 ; Maximum number of (minimization) steps to perform 
nstenergy = 10 ; Write energies to disk every nstenergy steps 

; 
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 
nstlist = 0 ; Frequency to update the neighbor list and long range forces 
ns_type = simple ; Method to determine neighbor list (simple, grid) 
rlist = 0 ; Cut-off for making neighbor list (short range forces) 
coulombtype = cut-off ; Treatment of long range electrostatic interactions 
rcoulomb = 0 ; long range electrostatic cut-off 
rvdw = 0 ; long range Van der Waals cut-off 
constraints = none ; Bond types to replace by constraints 
pbc = no ; Periodic Boundary Conditions (yes/no) 

eqb-invacuo.mdp 


define = -DFLEXIBLE 

constraints = none ; Bond types to replace by constraints 
integrator = md ;Algorithm options 
dt = 0.002 ; timestep for integration 
nsteps = 50000 ; Maximum number of steps to perform 100 ps 


nstxout = 1000 ; frequency to write coordinates to output trajectory 2 ps 
nstfout = 1000 ; frequency to write forces to output trajectory 2 ps 
nstvout = 1000 ; frequency to write velocities to output trajectory 2 ps 
nstxtcout = 1000 
nstlog = 1000 ; frequency to write energies to log 2 ps 
nstenergy = 1000 ; frequency to write energies to edr 




; Parameters describing how to find the neighbors of each atom and how to calculate the interactions 

nstlist = 0 ; Frequency to update the neighbor list and long range forces 
ns_type = simple 
rlist = 0 ; Cut-off for making neighbor list (short range forces) 
coulombtype = cut-off ; Treatment of long range electrostatic interactions 
vdwtype = cut-off 
rcoulomb = 0 ; long range electrostatic cut-off 
rvdw = 0 ; long range Van der Waals cut-off 
pbc = no ; Periodic Boundary Conditions (yes/no) 
epsilon_rf = 0 
rgbradii = 0 
comm_mode = angular 

comm-grps = system 

optimize_fft = yes 

; 

; V-rescale temperature coupling is on 

tcoupl = v-rescale 
tc-grps = system 
tau-t = 0.1 
ref-t = 300 

; 



; Pressure coupling is off 
Pcoupl = no 

; 
; Generate velocites is on 
gen_vel = yes 
gen_temp = 300 
gen_seed = -1 



; 
; Implicit solvent 

implicit_solvent = GBSA 
gb_algorithm = Still 
gb_epsilon_solvent = 80 
sa_surface_tension = 2.25936 

nstgbradii = 1 
rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist 

sa_algorithm = Ace-approximation 
sa_surface_tension = -1 








Best, 

Iris Nira Smith, Ph.D. Candidate 
Briggs Computational Biochemistry/Biophysics Laboratory 
University of Houston 
402E Health Science Center 
Houston, TX 77204 

A Carnegie-designated Tier One public research university 
Phone:281-726-0341 
Email: irisnsmith at comcast.net 
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