Re: AMBER: about MD outputs

From: <saccenti.cerm.unifi.it>
Date: Sun, 23 Sep 2007 14:34:00 +0200 (CEST)

MANY THANKS

paste & glue will destroy the world (and the wq command of vi too!)

Again many thanks!!!
Edo


> 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.cerm.unifi.it <saccenti.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.cerm.unifi.it <saccenti.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.scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" to majordomo.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
>>
>


-- 
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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Received on Mon Sep 24 2007 - 17:45:03 PDT
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