VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 05 2013 - 22:56:17 CST

On Fri, Dec 6, 2013 at 4:59 AM, Subbusinger N <subbu813_at_gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: Subbusinger N <subbu813_at_gmail.com>
> Date: Thu, Dec 5, 2013 at 5:32 PM
> Subject: dcd file uploading problem
> To: tutorial-l_at_ks.uiuc.edu
>
>
> Hi,
> This is Subrahmanyam,Research scholar, IIT Kharagpur. While uploading the
> dcd file to genrate rmsd file I got the following message of killing the dcd
> file.. This dcd file contains nearly 3400 frames. I tried on 32 bit it
> didn't work. It suggested me to use 64bit which gave me the following
> message while uploading. I tried to load dcd file by combining two dcdfiles
> of 1000 and 2400. kindly any of suggest how to proceed.

your system has 440466 atoms, for each atom you need 3*4 bytes of
storage to store the position in single precision, and then you have
3400 frames. if you put this together, you need: 440466*3*4*3400 bytes
= ~16.7 GB of RAM to store the coordinates alone. obviously, you don't
have that much, so the out-of-memory-killer procedure of the kernel
will kill VMD when you run out of memory.

axel.

p.s.: of course the 32-bit version will die earlier, since you only
have ~2GB of address space available.

>
>
>
>
>
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> 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, 4 CPUs detected.
> Info) Free system memory: 4826MB (82%)
> 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.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Mesa DRI Intel(R) Sandybridge Mobile
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (256x256x256), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> vmd > Info) Using plugin pdb for structure file
> /home/pad/Desktop/2PS1_wb.pdb
> Info) Using plugin pdb for coordinates from file
> /home/pad/Desktop/2PS1_wb.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 440466
> Info) Bonds: 296063
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 144914
> Info) Waters: 144460
> Info) Segments: 29
> Info) Fragments: 144468 Protein: 2 Nucleic: 0
> Info) Finished with coordinate file /home/pad/Desktop/2PS1_wb.pdb.
> psfplugin) Detected a Charmm31 PSF file
> Info) Using plugin psf for structure file /home/pad/Desktop/2PS1_wb.psf
> Info) Analyzing structure ...
> Info) Atoms: 440466
> Info) Bonds: 296054
> Info) Angles: 157384 Dihedrals: 18824 Impropers: 1136 Cross-terms: 444
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 144914
> Info) Waters: 144460
> Info) Segments: 29
> Info) Fragments: 144468 Protein: 2 Nucleic: 0
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Info) Using plugin dcd for coordinates from file
> /home/pad/Desktop/t2PS1_wb_eq.dcd
> Killed
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.