AMBER Archive (2007)

Subject: Re: AMBER: about MD outputs

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Sep 23 2007 - 07:31:06 CDT

yuo performed your minimization with setting ntb=0 (no periodic box).
anything after that won't work if you try to add the box back.
change ntb=0 in your min input to ntb=1.

On 9/23/07, saccenti_at_cerm.unifi.it <saccenti_at_cerm.unifi.it> wrote:
>
> Many thanks for reply
> I attach leap and minimization output log files:
>
> again many thanks in advance
> Edo
>
> > where did the input coordinates come from?
> They come from a minimization in water
>
> > what version of leap and sander are you using?
>
> -------------------------------------------------------
> Amber 9 SANDER 2006
> -------------------------------------------------------
>
> > did you build it as a periodic system? meaning did
> > you use solvatebox or something else to make
> > a periodic box when you built it?
>
> I use the command solvatebox
> >
> >
> > On 9/23/07, saccenti_at_cerm.unifi.it <saccenti_at_cerm.unifi.it> wrote:
> >>
> >> I'm just running my first MD on a 500ps timescale
> >> I'm concerned about this output:
> >>
> >> ntwr=5000,
> >> ntwx=1000,
> >> temp0=300.0,
> >> ntt=1,
> >> tautp=1,
> >> ntb=2,
> >> ntp=1,
> >> ntc=2,
> >> ntf=2,
> >> nrespa=1,
> >> cut=10.0,
> >> &end
> >>
> >>
> >>
> --------------------------------------------------------------------------------
> >> 1. RESOURCE USE:
> >>
> >>
> --------------------------------------------------------------------------------
> >>
> >> | Flags:
> >> getting new box info from bottom of inpcrd
> >> | INFO: Old style inpcrd file read
> >>
> >> | peek_ewald_inpcrd: Box info not found in inpcrd
> >> |Largest sphere to fit in unit cell has radius = 0.000
> >>
> >> This is the only file produced in 24h calculation.
> >>
> >> I run the following:
> >> /prog/amber9/exe/sander -O -i dinamica.in -o MNK1.dinamica.out -p
> >> prm_2.top -c MNK.system.rst -r MNK1.sys.din.rst -x MNK1.sys.din.crd
> >>
> >> There is come bug??
> >>
> >> Many thanks
> >> edo
> >>
> >>
> >> --
> >> Dr Edoardo Saccenti
> >> CERM Magnetic Resonance Center
> >> University of Florence
> >> Fiorgen Foundation
> >> Via Luigi Sacconi n° 6
> >> 50019 Sesto Fiorentino
> >> (FI) Italy
> >> Tel: +39 055 4574281
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>
> >
>
>
> --
> Dr Edoardo Saccenti
> CERM Magnetic Resonance Center
> University of Florence
> Fiorgen Foundation
> Via Luigi Sacconi n° 6
> 50019 Sesto Fiorentino
> (FI) Italy
> Tel: +39 055 4574281
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu