[gmx-users] Re: [gmx-developers] smalloc.c

[Yang Ye]

Yang Ye wrote:
> David van der Spoel wrote:
>> Patricia Soto Becerra wrote:
>>> Hi,
>>> I want to implement the rest algorithm (PNAS, 102, 39, 13749-13754. 
>>> (2005)). I have been following the discussions in the list of a very 
>>> similar implementation, particularly:
>>>
>>> http://www.gromacs.org/pipermail/gmx-developers/2006-January/001493.html 
>>>
>>> http://www.gromacs.org/pipermail/gmx-developers/2006-January/001494.html 
>>>
>>>
>>> Nevertheless, I get the error message:
>>> ______________________________________
>>> Source code file: smalloc.c, line: 113
>>> Fatal error:
>>> calloc for ir->opts.nrdf (nelem=1066665789, elsize=4, file tpxio.c, 
>>> line 487)
>>> -------------------------------------------------------
>>>
>>> I just cannot figure it out... Does anybody have a suggestion on how 
>>> to solve this?
>>>
>> there must be an inconsistency in your tpr file. Did you try to 
>> modify that?
> This mistake shall not be derived from the changes I suggested. This 
> is the changes I have made. They are declared to be under GPL.
>
> include/types/idef.h
> 1. in first enum    add    F_EPOT_NOSOL    after F_NRE
>
> include/tgroup.h
> 2. extern void sum_epot_nosol(t_grpopts *opts,t_groups *grps,real 
> epot[]);
>
> src/kernel/md.c
> 3. change snew(ener,F_NRE); to snew(ener,F_NRE+1);
> 4. replace
> sum_epot(&(inputrec->opts),grps,ener);
> to
> sum_epot_nosol(&(inputrec->opts),grps,ener); /*Fill in F_EPOT_NOSOL*/
> 5. replace
>    if ((repl_ex_nst > 0) && (step > 0) && !bLastStep && 
> do_per_step(step,repl_ex_nst))
>        bExchanged = 
> replica_exchange(log,mcr,repl_ex,state,ener[F_EPOT],step,t);
> to
>    if ((repl_ex_nst > 0) && (step > 0) && !bLastStep && 
> do_per_step(step,repl_ex_nst))
>        bExchanged = 
> replica_exchange(log,mcr,repl_ex,state,ener[F_EPOT_NOSOL],step,t);
>
> /src/mdlib/tgroup.c
> 6. add
> void sum_epot_nosol(t_grpopts *opts,t_groups *grps,real epot[])
> {
>  int i;
>  sum_epot(opts,grps,epot);
>  epot[F_EPOT_NOSOL] = epot[F_EPOT] - \
>                       (grps->estat.ee[egCOULSR][grps->estat.nn-1] + \
>                        grps->estat.ee[egLJSR][grps->estat.nn-1]   + \
>                        grps->estat.ee[egLJ14][grps->estat.nn-1]   + \
>                        grps->estat.ee[egCOUL14][grps->estat.nn-1] + \
>                        grps->estat.ee[egCOULLR][grps->estat.nn-1] + \
>                        grps->estat.ee[egLJLR][grps->estat.nn-1]   + \
>                        grps->estat.ee[egBHAMSR][grps->estat.nn-1] + \
>                        grps->estat.ee[egBHAMLR][grps->estat.nn-1]);
> }
>
> Regards,
> Yang Ye
>
Forgot this: above code takes as granted that last temperature coupling
group is solvent. It doesn't take the caution to check the group's content.

Yang Ye