[gmx-users] Regarding the Pi-Pi and pi-cation interaction

[rama david]

Dear Ivan,
       Thank you. I also think what you are saying that is right.
I will also goes through the article. Thank you for article

I actually run the system with simple Gromos96 5316 FF and amber 03 ff.  I
dont think it will
help me

With regards,
Rama David


On Thu, Oct 30, 2014 at 2:27 PM, Ivan Gladich <igladich at sissa.it> wrote:

> Hi,
> to the best of my knowledge,
> Molecular Dynamics is not the best way to study system stabilized by Pi-Pi
> or Pi-Cataion interaction.
>
> However,in MD  people usually overpolarized C-C and C-H bonds to
> increase the quadrupole interactions, and thus, mimic the Pi-Pi interaction
>
> See
> http://pubs.acs.org/doi/pdf/10.1021/jp408977b
> or
> http://pubs.rsc.org/en/content/articlelanding/2006/
> cp/b610253k#!divAbstract
>
> In conclusion (and in my opinion), you case use MD but be careful and test
> your Force field...
>
> Ivan
>
>
> On 2014-10-30 05:55, rama david wrote:
>
>> Dear Friends,
>>
>>  I search the archive to find the answer of my question but I did not get
>> satisfied answer so I am putting the question in forum.
>>
>> One of them is as
>> http://comments.gmane.org/gmane.science.biology.gromacs.user/51771
>>
>> I want to study the MD simulation of Ligand and Receptor that is stabilize
>> by
>>  Pi-Pi and pi-cation interaction
>>
>> 1.  Is it right to say the  Pi-Pi and pi-cation interaction can be studied
>> by Molecular    dynamics??
>>
>> 2.  Which force field I have to use ??
>>
>> 3. In the analysis tools I found that no direct tools can do this
>> directly.
>>     How to do this analysis
>>
>> I am looking forward for reply.
>>
>> With best regards,
>>
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