Re: AMBER: about MD outputs

From: <saccenti.cerm.unifi.it>
Date: Sun, 23 Sep 2007 14:23:15 +0200 (CEST)

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
>>
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>>
>


-- 
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 - 17:45:02 PDT
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