hi! I am doing some vacuum simulations with sander with constant
temperature. My problem is I see my protein moving whith a rotational
motion.
I found in the mail reflector some explaination about the ntcm or nscm flag:
"The only time you
should see significant numbers in the above message is after initial
random velocity assignment (which will likely lead to a small
translational componenet) of if energy is poorly conserved (due to
infrequent pairlist update, no buffered/skin pairlist, SHAKE tolerances
that are too low, time steps that are too large, ...)."
Indeed, I start my simulation with random velocity from the maxwell
distribution.
But the Non bonded pair list is updated every 10 steps (I assume it is
quite frequent)
So I stop using shake and I put my time step to 1 fentosecond
(previously 2 fento)
But even when I use nscm =1000, for the first printing step I see that
something happened :
"check COM velocity, temp: 0.011485 0.16(Removed)"
Next I never see something else that
"check COM velocity, temp: 0.000000 0.00(Removed)"
But when I watch my trajectory with VMD, I see the rotational motion.
And see the potential energy droping down progrisively, kinetic energy
is stable; so the total is droping down too.
I have several question :
Could you explain me why there is a lost of energy and is there anyway
to avoid that kind of motion?
Is it a problem for carnal or ptraj to do the RMSd calculation?
thanks
jean-françois TALY
Received on Thu May 22 2003 - 13:53:01 PDT
