Re: FW: simulation configuration file not accesible - other reasons

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 20 2009 - 18:37:51 CST

On Fri, Nov 20, 2009 at 6:57 PM, CHINDEA Vlad <vchindea_at_hotmail.com> wrote:
> Dear Richard
>
> I allways run with
>
> namd2 xxx.conf > yyy.log
>
> and it is not an issue of psf, pdb, param files (which BTW are exactly
> placed as suggested) because the program hangs up before needing any of
> these resources (as witnessed by log file).
>
> I think there has to be some other more obscure reason for this behaviour.

how about there being a file lock on xxx.conf due to being held open
in an editor and windows not giving your namd executable read access?

i don't use windows, but i remember some strange behavior about not
being able to manipulate files that are "locked" by some app before.

can you _read_ the xxx.conf file with something like "cat"?

cheers,
   axel.

>
> Regards
> Vlad
>
> ________________________________
> Subject: RE: namd-l: simulation configuration file not accesible - other
> reasons
> Date: Thu, 19 Nov 2009 17:38:15 -0600
> From: rowczarzy_at_idtdna.com
> To: namd-l_at_ks.uiuc.edu
>
> Did you specify your configuration file (e.g. run.conf) in command prompt?
>
>
>
> namd2.exe +p2 run.conf
>
>
>
> I usually copy namd2.exe and all input files in the same directory.
>
> You need:
>
> Namd2.exe
>
> Configuration file (e.g., run.conf)
>
> The files specified in configuration file:
>
> Structure file (*.psf)
>
> Coordinate file (*.pdb)
>
> Parameter file used to make psf (e.g., par_all27_prot_lipid_na.inp)
>
>
>
> You need to specify those files in the configuration file.
>
>
>
> Sincerely,
>
>
>
> Richard
>
>
>
> ________________________________
>
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of CHINDEA Vlad
> Sent: Thursday, November 19, 2009 4:46 PM
> To: NAMD list
> Subject: namd-l: simulation configuration file not accesible - other reasons
>
>
>
> Hi everybody
>
> I recently installed pre-compiled NAMD on a Windows platform but when trying
> to run tutorial sample files I get all the time the above message.
>
> Besides obviouse problems like path issues are there any other possible
> causes for this error ?
>
> I have tryed placing all simulation files in NAMD directory (which is
> declared in PATH variable), or used absolute paths but nothing works.
>
> Kind regards
> Vlad
>
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>
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-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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