[gmx-developers] md.c: do_force()

[Mitchell Stanton-Cook]

Hi,

I have been modifying orires.c to allow for continuation of time 
averaging runs.

In the current state, no time averaging data is stored and the restraint 
energy is reset when starting from a checkpoint.

In order to accomplish this task I have need to store- Dtav, xref, and 
exp_min_t_tau at checkpoints and re-initialise them .

Unfortunately I am having a problem as the coordinates get shifted on a 
re-run. I have tracked down what I believe is the offending code  to 
here (from L617 md.c - gmx331):

 else {
      /* The coordinates (x) are shifted (to get whole molecules) in 
do_force
       * This is parallellized as well, and does communication too.
       * Check comments in sim_util.c
       */
       
      do_force(log,cr,mcr,inputrec,nsb,step,&mynrnb,top,grps,
           state->box,state->x,f,buf,mdatoms,ener,fcd,bVerbose && !PAR(cr),
           state->lambda,graph,
           TRUE,bNS,FALSE,TRUE,fr,mu_tot,FALSE,t,fp_field,edyn);
    }

My question is -

Would there be any severe consequences of re-initialising the the 
coordinates to the checkpoint time values after calling this routine?



Cheers

Mitch

-- 
Mitchell Jon Stanton-Cook
PhD Student
Biomolecular modelling group
University of Queensland

m.stantoncook at uq.edu.au