VMD-L Mailing List

From: Jim Kress (jimkress_58_at_kressworks.org)
Date: Sat May 26 2012 - 15:47:08 CDT

I invoke VMD 1.9.1 and load a gromacs .xtc trajectory file. Here is the
cosole output:

Info) VMD for WIN32, 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, 12 CPUs detected.
Info) Free system memory: 4095MB (100%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] GeForce GTX 480 15 SM_2.0 @ 1.45 GHz, 1.5GB RAM, KTO, OIO, ZCP
Info) [1] Quadro FX 4800 24 SM_1.3 @ 1.20 GHz, 1.5GB RAM, KTO, OIO, ZCP
Info) OpenGL renderer: Quadro FX 4800/PCIe/SSE2
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFG)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
Info) No joysticks found. Joystick interface disabled.
Info) Dynamically loaded 69 plugins in directory:
Info) C:/Program Files (x86)/University of
Illinois/VMD/plugins/WIN32/molfile
Info) File loading in progress, please wait.
Info) Using plugin xtc for coordinates from file
W:\state\partition1\apps\usr\gr
omacs_4.5.5\bin\KALP\md_0_1__24_noPBC.xtc
Info) Finished with coordinate file
W:\state\partition1\apps\usr\gromacs_4.5.5\b
in\KALP\md_0_1__24_noPBC.xtc.
vmd >

I then load the data into the trajectory using the associated .gro file.
Here is the additionaI console output:

vmd > Info) Using plugin gro for structure file
W:/state/partition1/apps/usr/gro
macs_4.5.5/bin/KALP/md_0_1_24.gro
Info) Using plugin gro for coordinates from file
W:/state/partition1/apps/usr/gr
omacs_4.5.5/bin/KALP/md_0_1_24.gro
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 14017
Info) Bonds: 11361
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2672
Info) Waters: 2525
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 16 (protein) and 17 (none)
Info) Segments: 1
Info) Fragments: 2656 Protein: 1 Nucleic: 0
Info) Finished with coordinate file
W:/state/partition1/apps/usr/gromacs_4.5.5/b
in/KALP/md_0_1_24.gro.

I then use graphics > representation and create 4 reps: protein, lipids,
ions and water. As each is created, I assign them material values, coloring
methods, drawing methods and a trajectory smoothing size of 10.

I then visualize the trajectory. If I let VMD just sit for the next 45
minutes or longer, it becomes unresponsive.

I use speedfan to monitor all gpu and cpu temps. None exceed their normal
values. There is plenty of airflow through the workstation, so overheating
is not an issue. Testing of the system memory indicates no faults.

Why does VMD suddenly become unresponsive?

I do not have this problem with ANY other applications, even the ones that
use the gpus.

I have the latest drivers for the video cards.

Here is a summary of the specifications of the workstation:

[System Summary]

Item Value
OS Name Microsoft Windows 7 Professional
Version 6.1.7601 Service Pack 1 Build 7601
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name KRESSWORKST7500
System Manufacturer Dell Inc.
System Model Precision WorkStation T7500
System Type x64-based PC
Processor Intel(R) Xeon(R) CPU X5680 @ 3.33GHz, 3325 Mhz, 6
Core(s), 12 Logical Processor(s)
BIOS Version/Date Dell Inc. A11, 7/22/2011
SMBIOS Version 2.5
Windows Directory C:\Windows
System Directory C:\Windows\system32
Boot Device \Device\HarddiskVolume2
Locale United States
Hardware Abstraction Layer Version = "6.1.7601.17514"
User Name KressWorksT7500\Jim Kress
Time Zone Eastern Daylight Time
Installed Physical Memory (RAM) 12.0 GB
Total Physical Memory 12.0 GB
Available Physical Memory 7.05 GB
Total Virtual Memory 24.0 GB
Available Virtual Memory 18.9 GB
Page File Space 12.0 GB
Page File C:\pagefile.sys

[Display]
Operating System: Windows 7 Professional, 64-bit (Service Pack 1)
DirectX version: 11.0
GPU processor: GeForce GTX 480
Driver version: 301.32
DirectX support: 11
CUDA Cores: 480
Core clock: 725 MHz
Shader clock: 1451 MHz
Memory clock: 1900 MHz (3800 MHz data rate)
Memory interface: 384-bit
Total available graphics memory: 4094 MB
Dedicated video memory: 1535 MB GDDR5
System video memory: 0 MB
Shared system memory: 2559 MB
Video BIOS version: 70.00.21.00.82
IRQ: 24
Bus: PCI Express x16 Gen2
GPU processor: Quadro FX 4800
Driver version: 301.32
DirectX support: 10
CUDA Cores: 192
Core clock: 602 MHz
Shader clock: 1204 MHz
Memory clock: 800 MHz (1600 MHz data rate)
Memory interface: 384-bit
Total available graphics memory: 5119 MB
Dedicated video memory: 1536 MB GDDR3
System video memory: 0 MB
Shared system memory: 3583 MB
Video BIOS version: 62.00.70.00.09
IRQ: 0
Bus: PCI Express x16 Gen2

Jim