From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Wed Apr 28 2021 - 18:52:30 CDT
Hi mailing list,
First, does anyone know if there are plans to allow GPU support for constant-pH simulations?
I read that the computational expense of constant-pH simulations scales as the number of titratable sites (https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00875__;!!DZ3fjg!vkapbFNPDtn9CAiot_Whpx0neCWJlTuQyfFd0_biOaoipaJlsBMPzjtqWbF2YntEkQ$ ). My protein of interest has 65 titratable residues (127,352 atoms), but I only care about one. I have selected 8 more in the vicinity and used the keyword "cphExcludeResidue" to prevent the others from being considered, but my simulation is about the same speed after adding those exclusions (something like 300 cycles of 5 ps each in 20 hours for 9 replicas on 144 cores -- is this reasonable?). I am running namd2.13b2.
The documentation says the maximum number of switch proposal attempts per cycle defaults to the number of residues, so I lowered cphMaxProposalAttempts to 9. However, my log files all include the lines:
TCL: namdcph) CONSTANT pH neMD/MC MOVES:
TCL: namdcph) MAX. ATTEMPTS PER CYCLE: 1
TCL: namdcph) ONE RESIDUE MOVES
What is going on here? Is the log file wrong? Am I wrong to think that my simulations should speed up when less residues are considered for protonation events?
Best,
Harper Smith
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