AMBER Archive (2004)

Subject: Re: AMBER: Box information from Amber

From: Priti Hansia (
Date: Sat Oct 09 2004 - 12:51:16 CDT

hi carlos,

i am using amber7 and yes, i am using iwrap for my simulation. here is my
input for the simulation:

    ntx=7, irest=1,
    ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
    ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
    nstlim=5000, dt=0.002,
    tempi=300., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
    ntp=1, taup=0.5, npscal=1,
    ntc=2, tol=0.00001,

now, by 'box information from amber pdbs' i mean to say that i check the
maximum and minimum values of all the three coordinates in a pdb file and
i take the difference between the maxima and minima as the box size. for a
particular snapshot if i get these values as 86, 87, 100 approximately,
the corresponding values are 73.849 76.356 86.427 in the crd file. I dont
know if i am going wrong somewhere or misunderstanding things. Please

thanks and regards,

On Sat, 9 Oct 2004, Carlos Simmerling wrote:

> we need more info to help-
> are you using iwrap? if not, molecules may move out of the box (which
> is fine, the image molecules move in)
> also, where is the box in "amber pdbs", I wasn't aware that the pdb format
> fles that amber writes have box coordinates, maybe they do.
> are the furtherst atoms in a straight line along 1 axis? distances along
> the diagonal of the box can be longer.
> please be detailed- tell us which files, which amber version, and your
> input file.
> carlos
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web:
> Stony Brook, NY 11794-5115 E-mail:
> ===================================================================
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