I do it. but I got in output file info:
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = wiezy_3.in
LISTOUT = POUT
Restraints will be read from file: wiezy_3.in
Here are comments from the DISANG input file:
Number of restraints read = 1
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
Must have more residues than processors!
-----
I got this always, when my job is running [and after several second it killed].
best,
martha.
-----Original Message-----
From: Ross Walker <ross.rosswalker.co.uk>
To: 'AMBER Mailing List' <amber.ambermd.org>
Sent: Fri, 18 Mar 2011 14:54
Subject: Re: [AMBER] problem with gas-phase MD simulation in Amber8.
Set ntb=0. I also suggest setting cut=999.0 for a gas phase simulation.
> -----Original Message-----
> From: marta wiśniewska. [mailto:m.wisniewska.aol.pl]
> Sent: Friday, March 18, 2011 10:13 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] problem with gas-phase MD simulation in Amber8.
>
> hi,
>
>
> well, for what exactly I must change ntb? because I don't have any idea.
>
>
> best regards,
> martha.
>
>
>
>
>
>
> -----Original Message-----
> From: steinbrt <steinbrt.rci.rutgers.edu>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, 18 Mar 2011 9:23
> Subject: Re: [AMBER] problem with gas-phase MD simulation in Amber8.
>
>
> Hi,
>
> also, your input file had ntb=1, that is not a gas-phase simulation but a
> periodic box one. If you run that input file with a vacuum prmtop, your
> simulation will stop with an error.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Fri Mar 18 2011 - 12:30:01 PDT
