VMD-L Mailing List

From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Fri Apr 15 2005 - 12:24:00 CDT

So sorry for my insufficient information and thank you for your reply, John.

Those two VMDs are installed in separate machines. One VMD(ver 1.8.3) is
installed in a linux box and the other one (ver 1.8.2) is installed in
my windows laptop. I had had this problem in the VMD 1.8.2 in the linux
machine and I insatlled the 1.8.3 version in the linux, but I still have
the problem.

The similar probmem happens when I visualize the many water molecules
(there are only water molecules in the system) in the linux machine(ver
1.8.2). If I visualize a small number of water molecules, then that's
fine, but when I try to show the whole number of water molecules (around
1500 water molecules), wrong bonds beween an oxygen in one water and
hydrogens in another water are made and the picture is messed up.
Interestingly, this problem does not appear in the windows version
(1.8.2)of VMD.

The information of linux I'm using is :
Linux version 2.4.22-1.2188.nptlsmp (bhcompile_at_daffy.perf.redhat.com) (g
         cc version 3.2.3 20030422 (Red Hat Linux 3.2.3-6)) #1 SMP INTEL
Xeon dual processor 2.80GHz.

Thanks again.

-Hyon

John Stone wrote:
> Hi,
> Are you running both versions of VMD on the same machine (dual boot)?
> Or are these on different machines? What version of Linux are you running
> VMD on, and which version of VMD are you asking about. The more information,
> the easier it will be for us to help solve your problem.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Apr 15, 2005 at 11:14:43AM -0500, Hyonseok Hwang wrote:
>
>>Dear all,
>>
>>Sometimes the linux version of VMD shows wrong bonds and wrong bond
>>breaking of a molecule and messes up the molecule finally. But the
>>windows version of VMD shows the same molecule correctly. What's wrong
>>with my linux version of VMD. Do I have to install something?
>>Thanks a lot in advance!
>>
>>-Hyon
>
>