AMBER Archive (2005)

Subject: Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Tue May 31 2005 - 11:17:30 CDT

Grzesiek,
You haven't specified iwrap=1 keyword, which 'wraps' all molecules back
into the primary cell. maybe this is the cause??
Pozdrowienia
marcin krol

> Dear Amber 8 users,
> I created my system using LeaP provided with AMBER 8 distribution, and
> the old format of parameter file.
> During a short MD I ran using Amber 8 (and Amber 6), water molecules did
> not stay inside the box. This is something I didn't encounter using
> Amber 6's LeaP.
> Periodic Boundary Conditions were applied to a small hydrated DNA
> fragment neutralized with Na ions. When constant pressure was used, most
> of H20 "crept out" of the box like there were no PBC cell images. In
> contrast, when I used constant volume, single H2O molecules appeared far
> outside the box.
> When I ran 1 ns MD of a similar, but somewhat bigger system
> (volume=const.), water spread out over a large space, but empty spaces,
> corresponding to translational images of the solute, were left!
> I would say that no box information was passed in .TOP (parameter) file,
> but its last line says:
>
> 9.00000000E+01 3.95462090E+01 4.59628260E+01 3.57232720E+01
>
> Thank you for help
> Grzegorz Jezierski
>
> Below: input file for p=const (2nd stage of MD), and input for LEAP.
>
>
>
>
> # MD Ewald test
> #
> &cntrl
> ntb=2, imin=0, nmropt=0,
> ntx=5, irest=1,
> ntwx=1000, ntwv=1000, ntave=1000, ntwr=1000,
> cut=8.0, scnb=2.0, scee=1.2,
> ntt=1, tautp=0.4, TEMP0=298.0,
> dt=0.002, nstlim=10000,
> ntc=2, ntf=2,
> ntp=1,
> &end
> &ewald
> nfft1=40, nfft2=40, nfft3=40,
> order=4, ew_type=0,
> &end
> ==================================
> verbosity 2
> source leaprc.ff98
> set default OldPrmtopFormat on
>
> test = loadpdb test.pdb
> addions test Na+ 0
> solvatebox test TIP3PBOX 8.0
> saveAmberParm test test.top test.crd
> savePdb test test_NEW.pdb
>
> quit
>
>
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