[gmx-developers] Computing prot pot ener in the gmx code

[Yang Ye]

David van der Spoel wrote:

> pascal.baillod at epfl.ch wrote:
>
>> Hello,
>>
>> I thank you very much for your reply, David and Yang! May I ask you 
>> some more
>> details?
>>
>>
>>
>>> Add one more item after F_NRE
>>> This is one trick so that you just need to change the memory allocation
>>> in md.c to snew(ener,F_NRE+x); x is 1 for this case. If you put new 
>>> energy part before F_NRE
>>
>>
>>
>> 2) ..would this new energy part be F-EPOTprot (as re-used in my new 
>> routine
>> sum_epotPROT below)? Should I first define it, as you suggest, in 
>> idef.h, as:
>>
>> typedef atom_id t_iatom;
>>
>> /* this MUST correspond to the    t_interaction_function[F_NRE] in 
>> gmxlib/ifunc.c */
>> enum {
>>   F_BONDS,
>> /*  ......... a list of other contributrions*/
>>   F_DVDL,
>>   F_DVDLKIN,
>>   F_NRE,             /* This number is for the total number of 
>> energies    */
>>   F-EPOTprot         /* MY NEW CONTRIBUTION, after F_NRE */
>
>
> Put it before F_NRE.

What else shall be changed if placed before F_NRE. I got segmentation 
fault with mdrun when doing it last year. Pascal, could you get back us 
what do you get?
-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/