AMBER Archive (2003)

Subject: Re: translational and rotational motion (more information)

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu May 22 2003 - 08:35:13 CDT

This is a problem with vacuum simulations
in AMBER6. You should upgrade to AMBER7,
it has fixed this problem and has many other advantages.
I do not think that there is a simple bugfix for
this, but someone can correct me if I am wrong.
I can show you how to modify the code to fix
this but upgrading to AMBER7 is probably a
better choice.
Carlos

----- Original Message -----
From: "Jean-François Taly" <jftaly_at_jouy.inra.fr>
To: <amber_at_heimdal.compchem.ucsf.edu>; <carlos.simmerling_at_stonybrook.edu>
Sent: Thursday, May 22, 2003 9:25 AM
Subject: translational and rotational motion (more information)

>
>
> hi! I am doing some vacuum simulations with sander with constant
> temperature.
>
> I'm using AMBER6, whith no periodic condition.
>
> 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 I 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
>
>
> here my input file :
>
> &cntrl
>
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
>
> ntpr = 1000, ntwx = 1000, ntwr = 5000, ntwe = 1000,
>
>
>
> ntf = 1, ntb = 0, igb = 3,
>
> nsnb = 10, cut = 11.0,
>
>
>
> ibelly = 0, ntr = 0,
>
>
>
> imin = 0, nstlim = 250000,
>
> dt = 0.001,nscm = 1000, ndfmin = 6,
>
> ig = 71277,ntt = 1, tautp = 1.0,
>
>
>
> tempi = 10.0, temp0 = 300.0,
>
>
>
> vlimit = 20.0,
>
>
>
> ntc = 1, tol = 0.0005,
>
> &end
>
>
>