From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Thu Sep 22 2022 - 12:56:44 CDT
Question about standard deviations with MMPBSA. Should I use millions of snapshots for better standard deviations. I ran a 10 nanosecond simulation of my protein-peptide complex (2 fs timesteps, saved to dcd every 1000 steps). That would be 5,000 frames total in the DCD. I used CaFE and NAMD to get my MMPBSA result (single trajectory method). For CaFE I used stride 5 for the trajectory so that I would use a frame every 10 ps, thus a total of 1,000 frames for the MMPBSA calculation. My result is in the attached file. I get -29.3 kcal/mol with a standard deviation of 11.5. That's a large standard deviation. But, my standard error seems decent (11.5/sqrt(1,000) = 0.37), which appears to be what others report for these calculations instead of the standard deviation. So is this a good result for a single trajectory only using 1,000 frames for the calculation, or do I really still need to use millions of frames? Thanks!
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<https://urldefense.com/v3/__https://www.researchgate.net/profile/Kelly-Mcguire/post/MMPBSA_Results_Standard_Deviations_and_Standard_Errors/attachment/632a69160c295f1f9ad77097/AS*3A11431281085317296*401663723798950/download/MMPBSAResults.txt__;JSU!!DZ3fjg!_yU9Ko6sdHZlUdvq78zcZfgrQXILxuElkfj_rrsKGKNAAjLmm1ne44mZs0sgKioHGC4Rbwea414Dld2acveG9Q$ >
Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017
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