Jahanshah Ashkani,
PhD student of Biotechnology & Genetics,
University of the Western Cape,
Biotechnology Department,
Private Bag X17,
7735 Bellville,
Cape Town,
South Africa
[EMAIL PROTECTED]
----- Original Message ----
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Thursday, November 1, 2007 8:38:59 PM
Subject: Re: [gmx-users] CSDs
syawash Rezaei wrote:
> Hi there,
> I would be glad if you let me know how can I use a
> pdb file with CSDs in GROMACS.
and what might that be?
> Thank you very much.
> --- [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
>> Subject: [gmx-users] "Specified frame doesn't exist
>> or file not
>> seekable" when using .xtc
>> To: [email protected] <mailto:[email protected]>
>> Message-ID:
>>
>>
> <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
>> 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
>> -------------- next part --------------
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>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 01 Nov 2007 16:19:29 +0100
>> From: David van der Spoel <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
>> Subject: Re: [gmx-users] "Specified frame doesn't
>> exist or file not
>> seekable" when using .xtc
>> To: Discussion list for GROMACS users
>> <[email protected] <mailto:[email protected]>>
>> Message-ID: <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
>> 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.
>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
>> http://folding.bmc.uu.se
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 1 Nov 2007 16:27:39 +0100
>> From: "Qiao Baofu" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
>> Subject: Re: [gmx-users] "Specified frame doesn't
>> exist or file not
>> seekable" when using .xtc
>> To: "Discussion list for GROMACS users"
>> <[email protected] <mailto:[email protected]>>
>> Message-ID:
>>
>>
> <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
>> 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
>> <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>:
>>> 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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--
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.
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
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