[gmx-users] CSDs

[syawash Rezaei]

Hi there,
 I would be glad if you let me know how can I use a
pdb file with CSDs in GROMACS.
 Thank you very much.
--- gmx-users-request at gromacs.org wrote:

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> Today's Topics:
> 
>    1. "Specified frame doesn't exist or file not
> seekable"	when
>       using .xtc (Qiao Baofu)
>    2. Re: "Specified frame doesn't exist or file not
> seekable"	when
>       using .xtc (David van der Spoel)
>    3. Re: "Specified frame doesn't exist or file not
> seekable"	when
>       using .xtc (Qiao Baofu)
>    4. Re: "Specified frame doesn't exist or file not
> seekable"	when
>       using .xtc (David van der Spoel)
>    5. *.gro output file being written to inverse
> (Luciano Costa)
>    6. mdrun 3.3.2 crash - gmx_sumi called in serial
> run with	RF
>       (Michel Cuendet)
> 
> 
>
----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 1 Nov 2007 16:17:32 +0100
> From: "Qiao Baofu" <qiaobf at gmail.com>
> Subject: [gmx-users] "Specified frame doesn't exist
> or file not
> 	seekable"	when using .xtc
> To: gmx-users at gromacs.org
> Message-ID:
> 
>
<6a91f07b0711010817wb3e9454j7145001c33e8449d at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi, all
> 
> When I using the .xtc file to analyse, I always meet
> the following error
> information
>  Specified frame doesn't exist or file not seekable
> While it works when using the .trr file. In
> analyzing, only the coordinate
> is used. Therefore, I want to use .xtc file. In this
> way, it runs a little
> faster. However, the above proble exits.  What's
> wrong with the .xtc file?
> and how to solve it?
> 
> Thanks!
> 
> -- 
> Sincerely yours,
> Dr. Baofu Qiao
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> ------------------------------
> 
> Message: 2
> Date: Thu, 01 Nov 2007 16:19:29 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] "Specified frame doesn't
> exist or file not
> 	seekable"	when using .xtc
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <4729EE81.5010704 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> 
> Qiao Baofu wrote:
> > Hi, all
> > 
> > When I using the .xtc file to analyse, I always
> meet the following error 
> > information
> >   Specified frame doesn't exist or file not
> seekable
> > While it works when using the .trr file. In
> analyzing, only the 
> > coordinate is used. Therefore, I want to use .xtc
> file. In this way, it 
> > runs a little faster. However, the above proble
> exits.  What's wrong 
> > with the .xtc file? and how to solve it?
> > 
> gmx version please.
> > Thanks!
> > 
> > -- 
> > Sincerely yours,
> > Dr. Baofu Qiao
> > 
> > 
> >
>
------------------------------------------------------------------------
> > 
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> 
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol.,
> Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 1 Nov 2007 16:27:39 +0100
> From: "Qiao Baofu" <qiaobf at gmail.com>
> Subject: Re: [gmx-users] "Specified frame doesn't
> exist or file not
> 	seekable"	when using .xtc
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Message-ID:
> 
>
<6a91f07b0711010827y4611ed4ej309e0ebf5c67daed at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi,
> 
> I am using Gromacs 3.3.1.  The .xtc file is obtained
> from mdrun, as shown in
> the following
> 
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v)
> and forces (f)
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint            = 0
> ; Output frequency for energies to log file and
> energy file
> nstlog                   = 1000
> nstenergy                = 100
> ; Output frequency and precision for xtc file
> nstxtcout                = 10
> xtc-precision            = 1000
> 
> 
> 
> 
> 
> 2007/11/1, David van der Spoel
> <spoel at xray.bmc.uu.se>:
> >
> > Qiao Baofu wrote:
> > > Hi, all
> > >
> > > When I using the .xtc file to analyse, I always
> meet the following error
> > > information
> > >   Specified frame doesn't exist or file not
> seekable
> > > While it works when using the .trr file. In
> analyzing, only the
> > > coordinate is used. Therefore, I want to use
> .xtc file. In this way, it
> > > runs a little faster. However, the above proble
> exits.  What's wrong
> > > with the .xtc file? and how to solve it?
> > >
> 
=== message truncated ===


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