[gmx-users] how to output intramolecular pair interaction parameters

[Srinivasa Ramisetti]

Yes your right. I tested it and found the matrix is indeed based on the 
order of atom types.

Thank you
Srinivasa
On 16/11/2017 20:50, Justin Lemkul wrote:
>
>
> On 11/16/17 3:45 PM, Srinivasa Ramisetti wrote:
>> Exactly. I just wanted to know if we can get the order from the 
>> output information without calculating by hand as it is not always 
>> practical. Moreover, I am not sure if the order is preserved for each 
>> atom type. I will try this and let you know.
>
> The matrix is probably just being established based on the order of 
> parameters read. Do a simple test with 2 atom types, then 3, etc.
>
> -Justin
>
>> Thank you,
>> Srinivasa
>> Sent from my iPhone
>>
>> On 16 Nov 2017, at 20:26, Wes Barnett 
>> <w.barnett at columbia.edu<mailto:w.barnett at columbia.edu>> wrote:
>>
>> On Thu, Nov 16, 2017 at 3:07 PM, Srinivasa Ramisetti <
>> S.B.Ramisetti at leeds.ac.uk<mailto:S.B.Ramisetti at leeds.ac.uk>> wrote:
>>
>> This is continuation to my previous question. I used gmx dump to output
>> the 1-4 intramolecular interaction parameters. I could get the c6 and 
>> c12
>> values for all the list of 1-4 pair nteractions within my top file.
>> However, I could not understand the following lines in the output
>> information under the ffparams starting from functype[0] to 
>> functype[63]. I
>> do not understand how these 64 of c6,c12 values are related to 36 
>> atoms (8
>> atom types) that belong to my System. Could anyone explain me how can I
>> know which functype belongs to a particular atom/atom type?
>>
>>
>> You have 8 atomtypes, which means 8 sigmas and 8 epsilons . Here it 
>> is just
>> iterating through those atomtypes, combining the sigmas and epsilons
>> according to the combination rule in your force field, and then 
>> calculating
>> and storing c6 and c12 in memory (8x8=64). I'm not sure what order it
>> processes things in though. Try doing some of the combining by hand 
>> and see
>> what matches up.
>>
>>
>> -- 
>> James "Wes" Barnett
>> Postdoctoral Research Scientist
>> Department of Chemical Engineering
>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
>> Columbia University
>> w.barnett at columbia.edu<mailto:w.barnett at columbia.edu>
>> http://wbarnett.us
>> -- 
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>