actually, as far as i know, the -DFLEXIBLE argument has no effect on
simulations without explicit water ?!
i just copied the "define" line from my explicit simulation systems ..
so, the only define value, that has a meaning is -DPOSRESHELIX.
i didn't use constraints for the first time in my life since implicit
solvent simulations incorporate a much smaller number of atoms and are
therefore not that expensive computationally. i always use this setting
for my explicit simulations only in order to increase the step size to
2fs with a clear conscience ...
best wishes
vedat
Am 28.02.2012 15:18, schrieb Steven Neumann:
Thank you all!
How about -DFLEXIBLE in both em and md?
Steven
On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
lina wrote:
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann
<[email protected] <mailto:[email protected]>> wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your
simulation?
Otherwise, the system is easily explode with lots of LINCS
warning.
A system that is unstable will cause the LINCS algorithm to fail,
but turning off constraints does not prevent a system from
becoming unstable or crashing.
-Justin
Also thanks Vedat for sharing,
Best regards,
Steven
On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz
<[email protected] <mailto:[email protected]>> wrote:
hi steven,
i've been simulating a 33 AA peptide for the past two
days using implicent
solvent in order to achieve a proper folding.
i haven't added counterions, however, the systems
shows nice results
according to what i've expected. the mdrun command
(for the extension) for
our hardware looks as follows:
mpiexec -np 4 mdrun -pd -s md.tpr -append -cpi md.cpt
-deffnm md 2>&1
and here's the mdp file for the energy minimization:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.001 ; ps
nsteps = 30000
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all
(no cut-off), which
gets expensive for bigger systems
rcoulomb = 0
rvdw = 0
comm-mode = angular
comm-grps = Protein
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 5.0
emstep = 0.01
;
; Implicit solvent
;
implicit_solvent = GBSA
gb_algorithm = Still ; HCT ; OBC
nstgbradii = 1
rgbradii = 0 ; [nm] Cut-off for the
calculation of the Born
radii. Currently must be equal to rlist
gb_epsilon_solvent = 80 ; Dielectric constant for
the implicit
solvent
; gb_saltconc = 0 ; Salt concentration for
implicit solvent
models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension = -1
and for the md run:
define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES
constraints = none
integrator = md
dt = 0.001 ; ps
nsteps = 1000000000 ; 100000 ps = 100 ns
nstcomm = 10
nstcalcenergy = 10
nstxout = 1000 ; frequency to write
coordinates to output
trajectory
nstvout = 0 ; frequency to write
velocities to output
trajectory; the last velocities are always written
nstfout = 0 ; frequency to write
forces to output
trajectory
nstlog = 1000 ; frequency to
write energies to log
file
nstenergy = 1000 ; frequency to write
energies to edr file
vdwtype = cut-off
coulombtype = cut-off
pbc = no
nstlist = 0
ns_type = simple
rlist = 0 ; this means all-vs-all
(no cut-off), which
gets expensive for bigger systems
rcoulomb = 0
rvdw = 0
comm-mode = angular
comm-grps = system
optimize_fft = yes
; V-rescale temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1
tc_grps = system
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 ; HCT ; OBC
nstgbradii = 1
rgbradii = 0 ; [nm] Cut-off for the
calculation of the Born
radii. Currently must be equal to rlist
gb_epsilon_solvent = 80 ; Dielectric constant for
the implicit
solvent
; gb_saltconc = 0 ; Salt concentration for
implicit solvent
models, currently not used
sa_algorithm = Ace-approximation
sa_surface_tension = -1
best regards,
vedat
Am 28.02.2012 11:59, schrieb Steven Neumann:
Dear Gmx Users,
I am using Gromacs 4.5.4 and I would like to
implement implicit solvent
for folding of my protein. I read mailing list and
it is still confusing for
me.
Is it proper to use counterions within the system?
If not, how can I
obtain netral system?
Do we use cut off for vdw and coulombic interactions?
What kind of integrator should be used with a
timestep?
I will appreciate an mdp file for protein folding!
Thank you
Steven
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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