From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Tue Jul 24 2018 - 15:38:22 CDT
I'm still learning how to use colvars. As stated in other posts, the free energy in bulk water on one side of my membrane ion channel is about 30 kcal/mol higher than bulk water on the other side of the channel. We think this discrepancy is due to other orthogonal degrees of freedom needing to be biased. We would like to add a bias to some of the dihedrals in this channel. I have my usual distanceZ colvar set for the center of mass of the channel and the center of mass of the ligand.
Now, I am trying to add colvars for the dihedrals of four sidechains (channel is an homotetramer), the four histidine sidechains. That would be 5 colvars in my file. When I run the ABF, I get the error:
FATAL ERROR: Memory allocation failed on processor 0
If, I only do my distanceZ colvar and one of the dihedral colvars, then that error goes away, and then I get the error atom moving too fast...
What is causing both of those errors? Can I not have multiple dihedral colvars in the same file?
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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