[gmx-users] User-define non bonded table

Justin Lemkul jalemkul at vt.edu
Fri Jun 7 13:46:43 CEST 2013



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.sena at 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
>>
>> Thanks,
>> Mohan
>>
>>
>> On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann <s.neumann08 at 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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