VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Feb 09 2018 - 09:27:03 CST

First, check the output from the NAMD runs that are giving you the
connection error (if NAMD crashes before you can connect with VMD, it will
just look like a connection error). This will be in the autoimd.log file
(found by default in ~/autoimd). If NAMD is running fine and waiting for
the connection, check that you do not have multiple NAMD processes running
at the same time. If an IMD session is not killed correctly, NAMD may
continue to run and you can end up with many NAMD processes running at the
same time, which can cause problems, especially if they are looking at the
same port.

On Thu, Feb 1, 2018 at 4:18 AM De Winter Hans <Hans.DeWinter_at_uantwerpen.be>
wrote:

> Dear all,
>
> I am a newby in the use of VMD, so maybe my question was already posted
> and replied in this list (although I could not find a similar one in the
> archives). Currently I am reproducing the tutorial on 'Structure Check', in
> which the wrong chirality of some nucleic acids is corrected and the
> structure optimized using the 'Fix Chirality Errors' extension. This
> extension generates a temporary NAMD input file and then connects to NAMD
> using AutoIMD.
>
> The problem I have is that the execution is not reproducable, in which I
> mean that initially it all works fine, but after a couple of chirality
> fixes there seems to be a problem in connecting VMD with NAMD. The port on
> which these connect seems to vary, for example during the same session I
> got these two attempts:
>
> ERROR) Error connecting to localhost on port 2294
>
> and
>
> ERROR) Error connecting to localhost on port 5591
>
> Any clues? I am running VMD on Mac OS X, version 10.13.3 (High Sierra). I
> also tested it in our Ubuntu systems, but here we found no issues at all.
> So it seems to be OS X related.
>
> Many thanks in advance,
> Hans
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