VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Dec 11 2015 - 02:31:41 CST

Yes, that's a windows "feature". To change drives you have to enter "E:".
Or install Git for windows <https://git-scm.com/download/win> and you will
get a fully functional bash shell:)

Best,
Ajasja

On 11 December 2015 at 05:57, Ashar Malik <asharjm_at_gmail.com> wrote:

> As you can see when you do:
>
> *C:\Users\Julio>cd E:/VMD/nanotubes-files*
>
> your next prompt still reads this
>
> *C:\Users\Julio>*
>
> when it should read
>
> *E:\VMD\nanotubes-files>*
>
> 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>
> 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/
>> <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
>