There are therefore three possible reasons for this error message:ġ. This will, of course, only work if the particle type reveals the local secondary structure, which the MARTINI coarse-grain particles do.
Info) /usr/local/apps/VMD/1.9.3/lib/vmd/plugins/LINUXAMD64/molfileĪt this point you should see two VMD windows appear. Info) Dynamically loaded 2 plugins in directory:
Info) Full GLSL rendering mode is available. Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF) Info) OpenGL renderer: llvmpipe (LLVM 5.0, 256 bits) Warning) disable stereoscopic display when 'Composite' is enabled. Warning) try disabling this X server option. Warning) Detected X11 'Composite' extension: if incorrect display occurs Info) No CUDA accelerator devices available. Info) CPU features: SSE2 AVX AVX2 FMA KNL:AVX-512F+CD+ER+PF Info) Multithreading available, 4 CPUs detected. Info) Email questions and bug reports to Please include this reference in published work using VMD:
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) usr/local/apps/VMD/1.9.3/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /usr/local/apps/VMD/1.9.3/lib/vmd/vmd_LINUXAMD64) Salloc.exe: Nodes cn0851 are ready for ~]$ module load vmd Salloc.exe: Waiting for resource configuration Salloc.exe: Granted job allocation 13212187 Salloc.exe: job 13212187 has been allocated resources Salloc.exe: job 13212187 queued and waiting for resources Salloc.exe: Pending job allocation 13212187 Use the flag -cpus-per-task=# in your sinteractive command. If you expect to be running calculations with VMD, you may want to request more than the default 2 CPUs. Instead, start an interactive session and run the program. Please do not run VMD on the login node, which is shared by many users. Confirm that the graphics connection is working by typing 'xclock' - you should Once you have NX installed, open a session to Biowulf. Installing NX ( Installation Instructions). VMD is a graphics program, and therefore you need a graphics connection to Biowulf.
Running VMD in an interactive session on Biowulf