hi jan/steven (?),
you should know, in contrast to let's say justin lemkul, i haven't that
much experience with molecular simulations!
actually, i don't expect large differences in conformational/statistical
properties depending on the usage of lincs constraints. usually i use
them when simulating target ligand systems with explicit solvent in
order to save time. for these large systems (in the order of 100,000
atoms), i set emtol to about 300.
however, for this small peptide (33AA) i refrained from constraints and
set emtol to 5 which is achieved quite quickly. for a large protein with
implicit solvent i would probably set emtol to 50 or something like that.
according to your strange results:
i remember, i didn't do the energy minimization of the small peptide on
our computing cluster but on my local machine (six cpu-cores) with
gromacs-4.5.5 (no mpich, but openmpi). besides, i parameterized my
peptide using acpype (amber99sb force field) and didn't use editconf
(didn't set any box)! i just grompped the system and did the mdrun like
grompp -f ../em.mdp -c ../peptide.pdb -p ../peptide.top -o em.tpr
mdrun -v -deffnm em
and that's all .. 4 cores were used by mdrun.
hope, that helps
vedat
Am 28.02.2012 17:56, schrieb Steven Neumann:
I run energy minimization of my protein with implicit solvent:
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 = 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 = 2.25936
And I obtained:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 30000
Step Time Lambda
0 0.00000 0.00000
Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy = inf
Maximum force = 0.0000000e+00 on atom 0
Norm of force = nan
Can you please explain?
Steven
On Tue, Feb 28, 2012 at 2:29 PM, Vedat Durmaz <[email protected]
<mailto:[email protected]>> wrote:
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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