On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
Thank you Justin, now I understood. However, I do not have any target data
for my system. What do you suggest? the longer rcoulomb is safer, right?
Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
any specific value. It depends on your model. You have to demonstrate to
a skeptical audience that your methods are sound. That requires
describing a known system and its structure, energetics, and dynamics.
Then you can move to predicting unknowns. Without that, there's no
control to determine if your work is meaningful or a random number
generator.
-Justin
Best regards
On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
Thanks Justin. But I only define vdW potential form, coulomb potential
form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are
rlist = 0.9 (in nm)
rcoulomb = 0.9 (in nm)
fine while I am using PME?
Again, there is no standard value here and it is dictated by the
functional form being used. You have a custom interaction potential, even
if you're using normal PME alongside you have user-defined, tabulated vdW
interactions. Presumably there should be some evaluation of what cutoffs
are used to satisfy whatever the assumptions are in the parametrization of
your model, i.e. you need to have some target data of a known system that
tells you that your physical model (cutoffs and functional form) is right,
and then you use those same settings in whatever systems are of interest.
-Justin
Best regards
On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
Hi,
I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose
rlist
and rcoulomb correctly? (see below please)
I'm not sure if anyone can tell you that. You're using custom
potentials,
so setting cutoffs is part of the parametrization of that potential
itself.
-Justin
integrator = md
dt = 0.001
nsteps = 30000000
nstxout = 100000 ; save coordinates
every 0
ps
nstvout = 100000 ; save velocities every
0
ps
nstlog = 100000 ; update log file every
nstenergy = 100000 ; save energies every
nstxtcout = 100000 ; Output frequency for xtc
file
xtc-precision = 100000 ; precision for xtc file
ns_type = grid ; search neighboring grid
cells
nstlist = 10 ; fs
pbc = xyz ; 3-D PBC
rlist = 0.9 ; short-range
neighbor-list
cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic
cutoff
(in nm)
rvdw = 0.3479 ; short-range van der Waals
cutoff
(in nm)
coulombtype = PME-user ; Particle Mesh Ewald
for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
vdw-type = user
Tcoupl = berendsen ; modified Berendsen
thermostat
tc-grps = co2 rest ; two coupling
groups -
more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 179.8 179.8 ; reference temperature,
one
for
each group, in K
;tc-grps = system
cutoff-scheme =group
energygrps = co2 rest
Pcoupl = berendsen ;Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 6.2e-5
ref_p = 5500.0
gen_vel = yes
gen_temp = 179.8
gen_seed = 712349
DispCorr =no; EnerPres ; account for cut-off vdW
scheme
constraints = all-bonds ; all bonds constrained
(fixed
length)
continuation = no ; Restarting after NPT
constraint-algorithm = lincs ; holonomic constraints
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Best regards
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
