REMD with distance restrance
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I am trying to do REMD with distance restraints using gromacs-4.5.1. My problem is that if i specify the number of cores which are more than the number of tpr files that i have, my simulations are crushing with a segmentation fault. They seem to run very well if i specify the number of processors which are equal to the number of tpr files . I believe that is how REMD was meant work in versions prior to gromacs-4.0. If i run the same simulation without distance restraints, i can specify as many cores as i want and the simulations seem to run very well.
I am wondering if there is anything i am doing wrong,
I have tried to show the commands that i am using below...i am working with 16 replicas
1. mpprun -np 16 -pd -s md_tpr -multi 16 -replex 5000 -o md_
This one works fine with distance restraints
2. mpprun -np 64 -pd -s md_tpr -multi 16 -replex 5000 -o md_
The second one works fine without distance restraints but crushes with a segmentation fault when i use distance restraints.
My system is made up of two similar peptide molecules in a box. I have 36 nmr distance restraints on each of the peptides.
Thank you for your help
Updated code checks with distance restraints
Ensemble-averaged distance restraints require -multi, and it is
also reasonable to do REMD with distance restraints, which also
requires -multi. So checks for the ensemble-averaging case need
to be more sensitive to their context.
In fact, ensemble-averaging is probably functional only with PD and
one processor per system, since that was probably all that was
available when it was built.