Dear Amber Users,
I am attempting to simulate a protein in NVT, while saving the
configuration every 5ps using the langevin thermostat. My problem is I
found a drift in average total energy and am uncertain as to whether this
drift is due to some error on my part or solely due to the behavior of the
thermostat.
These ETOT values were collected by process_mdout.perl from the .out files
of 5 contiguous simulations of 20k frames each run via the input file
attached (md10.in).
Also attached is the xmgrace generated plot of the running ETOT average.
Does the total energy reported in the .out files include the restraint
energies (my system is heavily restrained on protein heavy atoms) and would
this contribute to this drift? Is there any blaring errors in my .in file
or my protocol (100ns while saving configurations every 5ps done 5x) which
could result in this drift?
For references sake the system was equilibrated in NPT conditions prior to
these production NVT simulations for ~1.4ns and the forcefields in use are
TIP3P for the water and AMBER99SB for the protein.
If any further information is required to help me understand this situation
I would be happy to provide that. Thank you for your time/ help, the
attachments referenced in the email can be found at this link.
https://www.dropbox.com/sh/rrlvs7rt3flglf8/AAB9kOFU4SMUt9lNNUBvfGs3a?dl=0
--Steven Ramsey
PhD Student Lehman College
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Received on Tue Apr 07 2015 - 07:00:02 PDT
