AMBER Archive (2003)

Subject: rotational and translational motion

From: Jean-François Taly (jftaly_at_jouy.inra.fr)
Date: Thu May 22 2003 - 07:45:18 CDT

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