[gmx-developers] Re: NMR refinement
mesanthu at gmail.com
Thu Jan 17 17:22:55 CET 2013
@Bogdan : I was able to figure that out and got a handle where I can input my
custom force code.
Just for future reference : this method implemented in the thread works,
I am having trouble figuring out something, here are my steps :
1). The simulation is run with -multi N, N simulations running parallelly.
(This is not replica exchange but a NMR refinement so -repex would *NOT* be
In the custom code I require the replicaID to be sent as a identification
and I am doing that by cr->ms->sim in md.c, (commrec.h has a struct
t_commrec which has gmx_multisim_t which has sim as the identification of
the replica). Please confirm that its right.
2). After every 1 step, I need to collect the current configuration of
selected atoms. ( For now I am thinking of making nstxtcout be 1 and use
trajconv to extract the last frame from that custom code) and compute force
using custom code.
But I am not sure that is how this command would run #mpirun -np 2 mdrun_mpi
-s test.tpr -multi 2
Since there is no place I am trying to sync both the replica's, both would
run independently and the custom force computation would be based on what
ever is the last written frame of the other replica(Need not be same step in
Is that right ? And any hints on trying to make sure that the replica's are
always in sync(same number of steps run in both the simulations) like NMR
refinement protocol is.
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