VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 30 2022 - 21:05:09 CDT
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impossible to say from this information.
you have about 4.5GB RAM available. with 437660 atoms at 12 byte coordinate
storage per atom, you should have sufficient space to load about 900 frames
from your trajectory file(s).
the memory consumption while loading the file(s) can be monitored with the
usual tools like top or htop.
On Wed, Mar 30, 2022 at 9:54 PM I. Camps <icamps_at_gmail.com> wrote:
> Hello,
>
> I am trying to load some trajectories from NAMD calculation. In the middle
> of loading, VMD just gets killed.
>
> My config is a Dell laptop running Ubuntu 2021.10, 64 bits with 8GB RAM
> and GPU Nvidia 1050Ti with 4GB RAM.
>
> Below is the info when loading the trajectory.
>
> Is this a memory issue?
>
> Regards,
>
> Camps
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> *Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18, 2021)Info)
> http://www.ks.uiuc.edu/Research/vmd/ <http://www.ks.uiuc.edu/Research/vmd/>
> Info) Email questions and bug reports to
> vmd_at_ks.uiuc.edu <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, 12 CPUs, ISA dispatch enabled.Info) CPU
> features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT Info) Free system memory: 4605MB
> (59%)Info) Creating CUDA device pool and initializing hardware...Info)
> Detected 1 available CUDA accelerator::Info) [0] NVIDIA GeForce GTX 1050 Ti
> 6 SM_6.1 1.6 GHz, 3.9GB RAM SP32 KT AE2 ZCInfo) OpenGL renderer: NVIDIA
> GeForce GTX 1050 Ti/PCIe/SSE2Info) Features: STENCIL MSAA(4) MDE CVA MTX
> NPOT PP PS GLSL(OVFGS) Info) Full GLSL rendering mode is available.Info)
> Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
> (4)Info) Detected 1 available TachyonL/OptiX ray tracing acceleratorInfo)
> Compiling OptiX shaders on 1 target GPU...Info) Dynamically loaded 3
> plugins in directory:Info)
> /software/vmd/plugins/LINUXAMD64/molfileafter#0vmd > psfplugin) Detected a
> Charmm PSF filepsfplugin) Detected a Charmm PSF EXTEnded fileInfo) Using
> plugin psf for structure file
> /home/icamps/Quantum_Chemistry/Yamini_Pathak/MD_outputs/01_1JDH_200ns.psfInfo)
> Analyzing structure ...Info) Atoms: 437660Info) Bonds: 436897Info)
> Angles: 157515 Dihedrals: 21174 Impropers: 1451 Cross-terms: 506Info)
> Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0Info)
> Residues: 144292Info) Waters: 142962Info) Segments: 4Info)
> Fragments: 143785 Protein: 1 Nucleic: 0dcdplugin) detected standard
> 32-bit DCD file of native endiannessdcdplugin) CHARMM format DCD file (also
> NAMD 2.1 and later)*
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!u0kCMaOK9FuZJUUjFMJfm3wPDQA7dPsjXYCuTwccSKnpKuZr-RJ1011fdPgD3w9Wkw$ College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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