Re: AMBER: Box information from Amber

From: Carlos Simmerling <>
Date: Sat, 09 Oct 2004 14:00:43 -0400

I think I understand, but keep in mind that iwrap only wraps molecules
if the center of the molecule moves out of the box, so a large molecule
might have many atoms outside the box edge (and it is still ok).

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:

Priti Hansia wrote:

>hi carlos,
>i am using amber7 and yes, i am using iwrap for my simulation. here is my
>input for the simulation:
> &cntrl
> imin=0,
> 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,
> cut=10.0,
> nscm=50,
> 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,
> &end
> &ewald
> vdwmeth=1,
> &end
>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 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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Received on Sat Oct 09 2004 - 19:53:00 PDT
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