VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon May 06 2013 - 07:57:36 CDT

AC,

There's no way for me to know how your server and/or job submission is done. You should check with your system administrator.

Regards,
Christopher Mayne

On May 6, 2013, at 12:31 AM, aravind chandrasekaran wrote:

Sorry.
Now that am using 1.9.2 version VMD, the .gau file contains input data.
Also, the .chk file (prld-opt.chk) is in the same folder as the .gau file in the server while running gaussian calculations. Does that make it accessible? Or should we mention the location of the prld-opt.chk file somewhere in the .gau file
Regs.,

On Sat, May 4, 2013 at 9:16 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
AC,

VMD-l is the listserv. Please keep this cc-ed so that others can benefit from my answering your question.

You didn't answer my first question--now that you are using the new ffTK version, does that .gau file contain information below the header?

If the job terminates after only 10 or so seconds, then it is most likely a file error. Make sure that the .chk file is accessible in the CWD where the calculation is run. If you are using a cluster that copies the files to a compute node where it is run from a different temporary file location, make sure that the .chk file also gets copied (this is generally done within a job submission script).

Regards,
Christopher Mayne

On May 4, 2013, at 5:52 AM, "aravind chandrasekaran" <gandhiaravind_at_gmail.com<mailto:gandhiaravind_at_gmail.com>> wrote:

Dear Christopher Mayne,
Sorry. I don't understand what listserv is.
The .gau file was generated from fftk associated with VMD 1.9.2
The job runs for around 10 second (wall clock time) before it quits.
Regs.,

On Fri, May 3, 2013 at 10:04 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
AC,

We should keep this discussion on the listserv.

This is a Gaussian error and not an ffTK error, so there's only so much insight I can provide.

1. Does your hessian .gau file written from the newer ffTK contain information below the header now that you're using the newest version of ffTK?
2. How long does the calculation run before the job terminates in error?

Regards,
Christopher Mayne

On May 3, 2013, at 1:27 AM, aravind chandrasekaran wrote:

Dear Christopher Mayne,
I downloaded the latest VMD version from BioCoRE and tried running Step 6. The .gau file that it generated, reported the following error in Gaussian.
Error termination in NtrErr:
 NtrErr Called from FileIO.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Google search of the error suggested that the maximum number of cycles have been reached and so the job has exited. How to fix this?
Thanks in advance,
Regs.,
AC. 

--
Aravind Chandrasekaran,
Research Scholar,
Computational Biology Lab,
National Tsing Hua University,
Taiwan.
http://140.114.98.99/wordpress/
--
Aravind Chandrasekaran,
Research Scholar,
Computational Biology Lab,
National Tsing Hua University,
Taiwan.
http://140.114.98.99/wordpress/