Fabian Casteblanco wrote:
Hello Justin,
You mean that only for vdW decoupling, you would need to use soft-core
potentials? I had soft -core potentials on for decoupling the
electrostatic interactions (see below). What would I use in its
place? Thanks again for your help!
You only need soft-core for LJ transformations. Set sc_alpha to 0 (as you have
noted in the comment) for normal (linear) interpolation.
-Justin
;Production MD
;------------------------------------------------------------------------------------
include =-I/mphase/users2/fabian/CGenff
title =CGenFF Lov/Eth Solution MD run
;PARAMETERS - describing what to do, when to stop and what to save
;------------------------------------------------------------------------------------
;Run parameters
integrator =sd ;leap-frog integrator
ld_seed =-1
nsteps =500000 ;2*500000=1000ps, 1 ns
dt =0.002 ;2 fs
nstcomm = 100 ;*** - frequency for center of mass
motion removal
;Output control
nstxout =1000 ;save coordinates every 2ps
nstvout =1000 ;save velocities every 2 ps
nstenergy =1000 ;save energies every 2 ps
nstlog =1000 ;update log file every 2 ps
nstxtcout =1000 ;xtc compressed trajectory output every
2 ps
xtc-precision =1000 ;*** - precision to write to xtc
trajectory
;Bond Parameters
continuation =yes ;Restarting after NPT
constraint_algorithm =lincs ;holonomic constraints
constraints =all-bonds ;all bonds (even heavy atom-H bonds)
constr;ained
lincs_iter =1 ;accuracy of LINCS
lincs_order =12 ;also related to accuracy
;Neighborhood searching
ns_type =grid ;search neighboring grid cells
nstlist =5 ;#steps. 5*0.002 ps = 5* 2 fs = 10 fs
- Frequency to
update the neighbor list (and the long-range forces, when
;using
twin-range cut-off’s). When this is 0, the neighbor list is made only
once.
rlist =1.1 ;short-range neighborlist cutoff (in nm)
rcoulomb =1.1 ;short-range electrostatic cutoff (in
nm)
pbc =xyz ; 3-D PBC
;Electrostatics
coulombtype =PME ;Particle Mesh Ewald for long-range
electrostat;ics
pme_order =4 ;cubic interpolation
fourierspacing =0.16 ;grid spacing for FFT
; van der Waals
vdwtype =Shift ;Van der Waals for CHARMM
rvdw_switch =0.8
rvdw =1.0 ;Short-range Van der Waals cut-off
;Dispersion correction
DispCorr =EnerPres ;account for cut-off vdW scheme
;Temperature coupling is on
tcoupl =V-rescale ;modified Berendsen thermostat
tc-grps =SYSTEM ;two coupling groups - more accurate
tau_t =0.1 ;time constant, in ps
ref_t =298 ;reference temperature, on for each
group, in K
;Pressure coupling is on
pcoupl =Parrinello-Rahman ;Pressure coupling on in NPT
pcoupltype =isotropic ;uniform scaling of box
vect;ors
tau_p =2.0 ;time constant, in ps
ref_p =1.0 ;reference pressure, in bar
compressibility =4.5e-5 ;isothermal compr of H2O,
ba;r^(-1)
; Free energy control stuff
free_energy = yes ;*** - Indicates we are doing a free
energy calculation, and that interpolation between the A and B states
of the ;chosen molecule (defined
below) will occur.
init_lambda = 0.0 ;*** - Value of λ
delta_lambda = 0 ;*** - The value of λ can be incremented
by some amount per timestep (i.e., δλ/δt) in a technique called "slow
;growth." This method can have
significant errors associated
with it, and thus we will make no time-dependent
;changes to our
λ values.
foreign_lambda = 0.05 ;*** - Additional values of λ for
which ΔH will be written to dhdl.xvg (with frequency nstdhdl). The
;configurations generated in
the trajectory at λ = init_lambda
will have ΔH calculated for these same
;configurations at all
values of λ = foreign_lambda.
sc-alpha = 0.5 ;*** - the soft-core parameter, a value
of 0 results in linear interpolation of the LJ and Coulomb
;interactions
sc-power = 1.0 ;*** - the power for lambda in the
soft-core function, only the values 1 and 2 are supported
sc-sigma = 0.3 ;*** - the soft-core sigma for
particles which have a C6 or C12 parameter equal to zero or a sigma
;smaller than sc_sigma
couple-moltype = LOV ;*** - name of moleculetype to decouple
couple-lambda0 = vdw-q ;*** - all interactions are on at
lambda=0
couple-lambda1 = vdw ;*** - only vdw interactions are on
at lambda=1
couple-intramol = no ;*** - Do not decouple intramolecular
interactions. That is, the λ factor is applied to only solute-solvent
;nonbonded interactions and not
solute-solute nonbonded
interactions.
nstdhdl = 100 ;*** - The frequency with which ∂H/∂λ
and ΔH are written to dhdl.xvg. A value of 100 would probably suffice,
since ;the resulting values will be
highly correlated and the
files will get very large. You may wish to increase this
;value
to 100 for your own work.
;Velocity generation
gen_vel =no ;Velocity generation is off
;END
On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
<fabian.castebla...@gmail.com> wrote:
Hello Justin,
I'm calculating the free energy of a drug in an alcohol solvent. I
have a question referring to your free energy tutorial. You mentioned
that decoupling of electrostatic interactions is linear and decoupling
of vdW can vary. Is this true for your case of methanol in water or
for all cases? When I ran my system of drug in ethanol solvent, I got
a non linear dG for both electrostatic and vdW. Also, is there no
need to find dG of cav ( the free energy required to form the solute
cavity within the solvent) ? I have attached some graphs.
Thanks for your help. Your tutorial was extremely useful.
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.castebla...@gmail.com
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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