When I finished REMD by amber 10 package, I tried to extract temperature trajectories. However, I can not extract the trajectory more than 200 ns even 300 replica exchange molecular dynamics simulations were carried out with a 2 fs time step. I supposed that it may be caused by the limitation of memory, but when I decreased the output frequency, I can only extract the frames in 200 ns. I checked the .mdcrd file and found something interesting. The first line of the first frame is " REMD 2 2 2500 285.590"
, but the first lines of the frames more than 200 ns are something like "REMD 2 67274 ******** 337.250“ . The ******** represent steps more than 1000000. How can I solve the problem?
I found the method to solve the problem in Amber Mailing List. The format for the trajectory files is only set to handle up to 100 million MD steps in a single run (between restarts). Perhaps you did a really, really long single run of REMD that led to
overflow of this value. you can change this bahavior in sander.f: write MDCRD_UNIT,'(a,3(1x,i8),1x,f8.3)') "REMD ", repnum,
mdloop, &
total_nstep, mytargettemp
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