AMBER Archive (2007)

Subject: Re: AMBER: about MD outputs

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Sep 23 2007 - 07:09:03 CDT

where did the input coordinates come from?
what version of leap and sander are you using?
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?

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
>
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