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
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>
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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Virginia Tech
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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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