FW: simulation configuration file not accesible - other reasons

From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Sun Nov 22 2009 - 15:04:27 CST

Hi Richard

Every time the simulation stops (in fact never starts) at:
" Info: Simulation configuration file is xxx.conf
Fatal error: Simulation configuration file not accessible"

OS is Windows XP and files are not compressed. I'll have to check regarding rights and file cache, but at least as a user I have complete RW rights to the disk.

I am also puzzled by this issue considering that I have been running NAMD with no issues for some time on another machine under Win XP.

Regards
Vlad

Subject: RE: namd-l: simulation configuration file not accesible - other reasons
Date: Sat, 21 Nov 2009 23:32:49 -0600
From: rowczarzy_at_idtdna.com
To: vchindea_at_hotmail.com

Where does it exactly hang? What is your OS, 32 or 64-bit? The error message says "file not accessible". Do you have unusual file system? Are files compressed? DId you remove file catching for c:\ hard disks? Does NAMD have rights to read the directory? Vista sometimes imposes weird file ownership/protections.
 
 I do not know origin of your problem; I am just brainstorming ideas. NAMD was targeted for Linux, so Win32 issues are not that surprising.
 
Precompiled win32 works fine for me. I run it for several weeks in Windows XP, Service Pack 2, 512MB memory, Pentium 4,NFST disks as well as in Windows 2000, 1GB memory, NFST disk machines. Both OS were 32-bit though. The only trouble is that the trajectory file (dcd) gets corrupted when it reaches 4GB size. Although NFST file system should handle larger files, NAMD cannot output it in my Win32 environments.
 
Wishing you good luck,
 
Richard

From: owner-namd-l_at_ks.uiuc.edu on behalf of CHINDEA Vlad
Sent: Fri 11/20/2009 5:57 PM
To: NAMD list
Subject: FW: namd-l: simulation configuration file not accesible - other reasons

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.

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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