Hi all,
I am trying to run QM/MM umbrella sampling using HREMD. However, all of the
simulations crash and the first replica in the groupfile gives the
following error:
Creation of partners array failed! Bad REMD setup!
Here's an example line from the groupfile:
-O -i r0/QMMM_1.inp -o r0/QMMM_1.out -p
../initial/ets_C41pC75p_Mg_QMMM_initial.prmtop -c r0/QMMM_0.rst7 -r
r0/QMMM_1.rst7 -x r0/QMMM_1.nc -rem 3 -remlog QMMM_1.remlog
Poking around in the source code it looks like the error message is
triggered when checking that all replicas have 2 defined replicas. Under
what circumstances would/should this check fail? It seems like a pretty
foolproof process based off of reading the groupfile.
Thanks,
Brian
P.S. Disclaimer: This is being run with a version of AMBER12 that I
compiled myself on Kraken (to be sure that the latest QMMM fixes are
applied). I haven't been able to verify all of the test suites just yet
since Kraken has no test/development queue.
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Feb 01 2013 - 16:00:03 PST
