[gmx-users] nonbond_params

[Amir Marcovitz]

Thank you Justin,

I didn't understand though where can I edit the [ nonbond params ] section?
Is there a better way to define pairs with no LJ attraction that will ignore
the settings in the *nb.itp file?

Cheers,
Amir

On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amir Marcovitz wrote:
>
>> Hi,
>>
>> my system is composed of two molecules, each is composed of a 36 carbon
>> like dummy atoms i defined in the amber files (i.e., has the LJ parameters
>> of a carbon)
>> I'm interested in eliminating the attractive Lennard-Jones interactions
>> between the dummy atoms , such that only the repulsive terms will account.
>>
>> I thought of adding a section to the *.top file:   [ nonbond params ] and
>> to set c6 to 0 such that the attractive term of the LJ is eliminated.
>> I used exactly the same syntax of the tutorial (page 98):
>>      * D     D        1       0.00000E-00       0.34252E-05*      ; (D is
>> just the name of my dummy atom)
>>
>> but got a syntax error when running grompp:
>> *Fatal error:
>> Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642
>> Last line read:
>> '[ nonbond_params ]'
>> Invalid order for directive nonbond_params*
>>
>> 1) what is wrong with my syntax? are there any further examples anywhere
>> for the usage of  [ nonbond params ] in topology files?
>>
>
> If you have already #included a force field file in the .top, it will have
> a [nonbond_params] section in it already.  You cannot add a new one.  The
> proper approach would be to modify the #included *nb.itp file.
>
>
>  2) Is [ nonbond params ] the right strategy to the task i described?
>>
>>
> Sounds like one way to do it.
>
> -Justin
>
>  Many Thanks,
>> Amir
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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