[gmx-users] Regarding obtaining potential energy using energy groups

[David van der Spoel]

Den 2019-09-14 kl. 23:32, skrev Najamuddin Memon:
> It depends on interaction of proteins i.e A interacts with B
> A&B both interact with C
> Only A or only B interacts with C
> In 2nd option you can make one group (A&B) and 2nd group as C

Note that this only tells you about non-bonded interaction at short 
range. In order to also include the long range (PME), checkout this 
paper: J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013) (supporting info 
in particular).
Then you still do not have grouped energies for the bonded forces since 
this is not implemented and finally you have to ask yourself what does 
an interaction energy mean?

> 
> On Sun, Sep 15, 2019, 12:28 AM Nashit Jalal 17250017 <
> nashit.jalal at iitgn.ac.in> wrote:
> 
>> I think so that the question is to confirm whether finding potential energy
>> making (AB) and C as 2 groups similar to the potential energy obtained by
>> adding energies obtained by making A -C and B -C as groups
>>
>> -Nashit
>>
>> On Sun, Sep 15, 2019 at 12:10 AM Najamuddin Memon <
>> najamuddinmemon63 at gmail.com> wrote:
>>
>>> No you should take two groups at a time
>>> Like A VS B then A vs C and so on before doing energy analysis you should
>>> make index file that you have to call in command line with -n index.ndx
>>> Regards
>>> Najam
>>>
>>> On Fri, Sep 13, 2019, 3:21 PM Nirali Desai <
>> nirali.d.imsc14 at ahduni.edu.in>
>>> wrote:
>>>
>>>> Dear all
>>>> I have a system with 3 protein chains A B and C. I want to calculate
>> the
>>>> potential energy between different chains.
>>>> I created energy groups by creating a new index file.
>>>> If I calculate potential energy between  C as one group and (AB) as
>>> another
>>>> group, will it contain the potential energy of interaction between A
>> and
>>> B
>>>> too?
>>>>
>>>> Your kind guidance in this matter is highly appreciated.
>>>>
>>>>
>>>> Thanking you,
>>>> Nirali Desai
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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