VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Dec 11 2015 - 03:52:26 CST

W dniu 11.12.2015 o 05:57, Ashar Malik pisze:
> As you can see when you do:
>
> *C:\Users\Julio>cd E:/VMD/nanotubes-files*
> *
> *
> your next prompt still reads this
> *
> *
> *C:\Users\Julio>*
This is ancient knowledge nowadays - the DOS commands :)
This behaviour is the feature of the cmd command interpreter - the
current folder has been changed for disk E:, but the current disk is
still C:.
To change the current disk, you must issue another command:*

e:
*
(yes, just this). Then you should see the expected prompt:
*
E:\VMD\nanotubes-files>*

and also NAMD will work on e: in the folder you wanted and will be able
to find the input file there.
Cheers,
Pawel

> *
> *
> in short your attempt at changing path doesn't work. Meaning when you
> run NAMD, it tries to look for the conf file in the wrong folder and
> hence fail.
>
> Solution: Make sure you are in the same folder as your conf file
> before you run NAMD.
>
>
> On Fri, Dec 11, 2015 at 12:36 PM, Julio Cantu
> <julio.c.cantu03_at_utrgv.edu <mailto:julio.c.cantu03_at_utrgv.edu>> wrote:
>
> Hello all,
>
>
>
> I am attempting to follow the nanotubes tutorial, but have trouble
> when submitting my own namd job. I receive the following error
> once I initiate the simulation:
>
>
>
> *C:\Users\Julio>cd E:/VMD/nanotubes-files*
> *
> *
> *C:\Users\Julio>E:/VMD/NAMD/namd2 sim_short.conf*
> *Charm++: standalone mode (not using charmrun)*
> *Charm++ warning> fences and atomic operations not available in
> native assembly*
> *Converse/Charm++ Commit ID:
> v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-De*
> *c-08-28969*
> *[0] isomalloc.c> Disabling isomalloc because mmap() does not work*
> *CharmLB> Load balancer assumes all CPUs are same.*
> *Charm++> Running on 1 unique compute nodes (4-way SMP).*
> *Charm++> cpu topology info is gathered in 0.000 seconds.*
> *Info: NAMD 2.10 for Win64-multicore*
> *Info:*
> *Info: Please visit http://www.ks.uiuc.edu/Research/namd/*
> *Info: for updates, documentation, and support information.*
> *Info:*
> *Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802
> (2005)*
> *Info: in all publications reporting results obtained with NAMD.*
> *Info:*
> *Info: Based on Charm++/Converse 60601 for multicore-win64*
> *Info: Built Tue, Dec 09, 2014 3:31:31 PM by jim on europa*
> *Info: Running on 1 processors, 1 nodes, 1 physical nodes.*
> *Info: CPU topology information available.*
> *Info: Charm++/Converse parallel runtime startup completed at 0 s*
> *Info: 4.49219 MB of memory in use based on GetProcessMemoryInfo*
> *Info: Configuration file is sim_short.conf*
> *FATAL ERROR: Unable to access config file sim_short.conf*
> *------------- Processor 0 Exiting: Called CmiAbort ------------*
> *Reason: FATAL ERROR: Unable to access config file sim_short.conf*
> *
> *
> *Charm++ fatal error:*
> *FATAL ERROR: Unable to access config file sim_short.conf*
> *
> *
> *
> *
> I apologize if the solution if trivial, but if anyone may have
> some insight as to what I am doing wrong, I would greatly
> appreciate it.
>
>
> Thank you for your time and consideration.
>
>
> Julio
>
>
>
>
> --
> Best,
> /A