

AMBER Archive (2006)Subject: AMBER: some puzzles in equilibration MD From: Zhihong Yu (computation_at_mail.nankai.edu.cn)Date: Mon Oct 09 2006  08:58:06 CDT
Dear All,
Now I'm running a equilibration MD using PMEMD.MPI (version 9), as usual, I did the equilibration in two step:
inupt file of STEP 1 is as follow:
equilibration md1
gamma_ln = 5.0, (REMARKS: if I use 1.0 only, the RMS of temperature is 68.96K, AVERAGE is 369.46K, the largest value is 478.01K, so I use 5.0, the result got better, RMS decreased to 26.16K, AVERAGE is 319.46, the largest value is 396.96K. In fact, I think the temperature contorl is not very satisfactory, what should I do? just keep increasing gamma_ln to 10.0 or do something else?)
nstlim = 20000,
dt = 0.001, (REMARKS: I used dt = 0.002 at the beginning, but when the MD went to 398 step, error of "vlimit exceeded for step 398; vmax = 128.7932, Coordinate resetting cannot be accomplished, deviation is too large" took place, so I decreased it to dt = 0.001, and restrained the solute only by 2.0 force constant, then the MD could complete. But, when I checked the md out file, I found many many "vlimit exceeded for step" warnings have appeared from beginnig to ending, so I wondered whether this equilibration MD is valid? Can I perform the second NTP equilibration MD based on this MD results? )
ntpr = 200, ntwx = 200, ntwr = 1000
Any advice will be greatly appreciated! Thanks in advance & Best regards!
yours sincerely, Zhihong Yu

 
