AMBER Archive (2000)

Subject: Re: IBELLY

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Thu Mar 09 2000 - 13:46:41 CST

dear marios
It appears you are running constant pressure with belly. Actually the
BELLY option just insures that AMBER forces due to the other atoms are
all zero on the nonbelly atoms, and that these "frozen" atoms don't have
an initial velocity. If you run constant pressure, you are at
any time step moving all molecules to expand or contract the whole
system. (I can't see any way to avoid moving all molecules in this
step) Since the molecules move rigidly in the pressure step this may be
ok for some belly simulations. In your case I however would use
positional restraints, or better an ion-ion distance constraint while
equilibrating.
hope this helps
Tom Darden

On Thu, 9 Mar 2000, Marios Philippopoulos wrote:

> Does IBELLY really freeze the cartesian coordinates of the specified
> groups during dynamics?
> I just checked the coordinates of the "frozen" atoms in my restart file
> prior to the dynamics run and in the first frame written out in the
> trajectory file, and they differ in the two files. I have two "solute"
> ions in a box of water.
>
> My input file is the following:
>
> ---------------------
>
> NpT equilibration of solvent only - 50 ps heating and dynamics
> &cntrl
> imin=0, irest=0, ntx=1, scee=2.0, cut=9.0,
> tempi=0., ntt=1, temp0=300., tautp=0.2,
> ntp=1, taup=0.2,
> ntb=2, ntc=2, ntf=2, ibelly=1, dt=0.002,
> nstlim=50000,
> ntwe=500, ntwx=100, ntpr=25, iwrap=1, ntcm=1,
> &end
> Allow only solvent to move; fix solute atoms:
> RES 3 777
> END
> END
>
> -----------------------
>
> In the output file BELLY seems to be applied to the right atoms:
>
> -----------------------
> ........
> LOADING THE BELLY ATOMS AS GROUPS
>
> ----- READING GROUP 1; TITLE:
> Allow only solvent to move; fix solute atoms:
> GRP 1 RES 3 TO 777
> Number of atoms in this group = 2325
> ----- END OF GROUP READ -----
> -----------------------
>
> I have also measured the distance between the two solutes and it has
> changed as well in the course of the trajectory.
> Has anyone else seen this?
>
> Thanks,
>
> Marios Philippopoulos
>
>
>
>
>
> --
> Marios Philippopoulos, PhD
> Structural Biology and Biochemistry Programme
> Hospital for Sick Children
> 555 University Avenue
> Toronto Ontario Canada M5G 1X8
>
> mphilip_at_sickkids.on.ca
>
>
>