VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 18 2000 - 18:49:25 CDT

Hi,
  We fixed a bug in VMD which caused the problem that you are
experiencing. If you try VMD 1.5a2 the VMD side of the code has
the fix in place. I don't remember off of the top of my head if
the NAMD side required any change or not, but try VMD 1.5a2 first,
and see if that fixes the problem. I'm out of the office until
Friday, so I can't really give you much more detail on this until
I return, but in the mean time 1.5a2 is your best bet.

Let us know if you still have the problem with 1.5a2, and the
same rev of NAMD...

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 18, 2000 at 06:35:03PM -0400, John Duff wrote:
> Hello,
>
> I'm a CS grad student at Michigan Tech University, and am having a problem
> getting VMD to connect properly to a running NAMD simulation on Linux.
> (on Sun/Sparc systems, I can do it no problem.) Here's the situation:
>
> Setup: RedHat Linux 6.2 (latest versions of everything) on a
> Dell Inspiron 7000 laptop (366 MHz Pentium II) 128M RAM
>
> Description: I downloaded and installed NAMD_2.1_Linux-i686 and
> VMD 1.4 (vmd-1.4.bin.LINUX.mesa.tar.gz). For VMD, I ran the
> configure script (after changing the install directories, nothing
> major) and then did a 'make install', as per the README file
> instructions. VMD runs fine on its own, I can load the sample
> alanin molecule and rotate/animate/see it no problem. Similarly,
> I can run NAMD just fine using the provided sample alanin
> files. So, running them each separately works beautifully.
> But, when I tried to attach VMD to a running NAMD simulation,
> (both running on the same machine, my laptop), VMD gives a
> warning message in the console popup window about
> "Connecting to opposite-endian machine", then the alanin molecule
> I had already loaded into VMD (as per the directions, and I can
> rotate/animate/see it no problem) basically explodes in the
> viewport (sounds over dramatic, but best way to describe it)
> and then VMD coredumps and NAMD also stops. I have no
> problem doing this (attaching VMD to running NAMD sim) on a
> Sun Ultra 5, so I know that my NAMD alanin file is set up
> correctly, and I'm following the directions correctly as well.
> The error message about opposite-endianness seems to be a clue
> to me, because that shouldn't be if both are running on the
> same machine, obviously. Is this all due to some known issue?
> I looked over the email archives, but didn't see
> anything useful (maybe I missed it?). I noticed some postings
> about having to use older versions of glibc in older versions
> of VMD, but assumed that since VMD runs fine on its own for me
> that that was not the problem.
>
>
> Any help or pointers anyone could offer would be greatly appreciated. If you
> need any more info from me, please let me know.
>
> Thanks in advance,
> John Duff
> jfduff_at_mtu.edu
>
> 

-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
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