VMD-L Mailing List

From: John Duff (jfduff_at_mtu.edu)
Date: Wed Apr 19 2000 - 10:25:46 CDT

John,

Excellent! That did the trick. After downloading and running VMD 1.5a2,
I was able to connect to a running NAMD sim (same version of NAMD that I
had been using, 2.1) on my linux box.

Thanks again,
John

>
> 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
> >
> >
>