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Re: [ESPResSo-users] Problem with vmd

From: Owen Hickey
Subject: Re: [ESPResSo-users] Problem with vmd
Date: Thu, 12 Mar 2015 11:18:00 +0100

Hey Nairhita,

Espresso and VMD are actually two separate projects and this seems to
be coming from VMD, which has its own mailing list. I might suggest
asking on that mailing list as they are more likely to have the
necessary expertise to solve this issue. Since no window appears, I
wonder if you ssh'ed using -X? This is necessary in order to generate
gui windows when using ssh. Another option would be to first write out
all of the particle properties you want to visualize using the
blockfile command:
    set f [open $file "w"]
    blockfile $f write variable box_l
    blockfile $f write particles {id type q pos v f}
    blockfile $f write bonds
if you produce all the necessary snapshots this way on the cluster,
you can then copy the files onto your local machine, and load the
blockfiles with:
    set f [open $file "r"]
    while {![eof $f]} {blockfile $f read auto}
    close $f
This would solve the problem of trying to run VMD remotely on the
cluster. The last option would be instead to output the snapshots in
VTK format and read them with Paraview. This last option would be my
recommendation as I find Paraview significantly easier to use than

Hope that helps!


On Tue, Mar 3, 2015 at 10:13 AM, Nairhita Samanta <address@hidden> wrote:
> Hi all!
>           I installed vmd in the our cluster, as Espresso is also in that
> system. But when I give the command vmd in terminal the following message
> appears
>  Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> Info)
> Info) Email questions and bug reports to address@hidden
> Info) Please include this reference in published work using VMD:
> Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 80 CPUs detected.
> Info) Free system memory: 78551MB (97%)
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> and no window appears. Can anyone help me with this and suggest a solution.
> Regards,
> Nairhita

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