Dear Amber users:
I have been runing some MD runs of small peptides (8 aa) in a water box,
using periodic boundery condictions. I've tryed to run for a 1ns period
with a time step of 1fs (using shake for bonds involving H atoms, NPT
ensamble simulation with privious mdrun in NVT ensamble). I was trying
these simulations at diferent cutoffs and both of mdruns "died" at
exactly the same step! There was none error message in the Sander output
file! My question is, is there any limit to the number of steps on a MD
in sander ?
Another thing: while looking at the mden file (energy data over the
trajectory) from these runs, we've noticed there was three diferent
types of pressure: pressure; Pres_scal_solu and Pres_scal_solv (I'm
using Berendsen barostact). My guess is that pressure is refering to the
instant pressure, but I haven't still found any reference to confirm
this! I used pres0=1.0 and Pres_scal_solv in around that value during
the simulation run! Is this the value of pressure under Berendsen
Pressure control? What do Pres_scal_solv and Pres_scal_solu refer to?
Sorry for these naive questions and thanks you for all your attention
and replies!
Sincerely yours
Marco A. C. Preto (Ph.D student)
Theoretical Chemistry group
Chemistry Department - FCUP
Porto, Portugal
Received on Wed May 07 2003 - 16:53:01 PDT
