AMBER Archive (2003)

Subject: Re: rotational and translational motion

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu May 22 2003 - 07:54:51 CDT

In this case it is important to tell us which
AMBER version you are using and whether
it is a periodic simulation or not. I believe that
AMBER 6 did not remove rotational motion for
GB simulations; this may be the problem. If you
are using AMBER7 then you should also send
your input file.
Carlos

----- Original Message -----
From: "Jean-François Taly" <jftaly_at_jouy.inra.fr>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, May 22, 2003 8:45 AM
Subject: rotational and translational motion

> 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
>
>
>