On 6/7/13 10:33 AM, Steven Neumann wrote:
It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
That may be an erroneous statement. Within very short distances, you will have
nearly infinite forces, so zeroes are used instead since these distances should
never occur. There's nothing wrong, per se, with entering really huge numbers
for short distances.
The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some values so the potential will equal zero?
The table entries must continue until rc + 1 nm, where rc is the longest cutoff
specified in the .mdp file.
-Justin
On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann <s.neuman...@gmail.com>wrote:
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x)
and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
or
[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05
Or maybe both?
Try the tutorial first and make sure you can replicate it. If you're
just looking to tweak C6 and C12 parameters, there's no need for tabulated
functions at all.
-Justin
I want to change function g(x) to use Chandler Anderson potential so g(x)
= 1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?
On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why they
start
from x=0.04? Why not 0.02 or sth else?
You can start the table from whatever value of x that you like, but
at a
certain point, it is unlikely that particles ever come that close, given
normal repulsive potentials.
-Justin
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
<maruthi.s...@gmail.com>wrote:
Hi Neumann,
You can use tabulated potential option
in
gromacs. Please check the site given below:
http://www.gromacs.org/****Documentation/How-tos/****
Tabulated_Potentials<http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials>
<http://**www.gromacs.org/Documentation/**
How-tos/Tabulated_Potentials<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials>
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann <s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish
to
set
it up for all atoms with same potential. Is there any example of the
table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that
right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
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Justin A. Lemkul, Ph.D.
Research Scientist
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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