VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue Jan 30 2024 - 10:12:10 CST

I'm confirming the Windows issue reported by Alexei.
NAMD 2.14 for Windows will not read files larger than 2Gb. (Learn more here
https://urldefense.com/v3/__https://en.wikipedia.org/wiki/2_GB_limit__;!!DZ3fjg!_TJBV_nFUFKFpf5GSWdC2xPW936mrT53e_5evufUnisAE5Yqitu3B1aVmW-CG30yrwGN6x4MAc7F9NumZ87E$ )
Don't worry, I'll bug NAMD developers to fix it.

A quick workaround is to use WSL (Windows Services for Linux).

I tried it this morning, and I'm glad to say that NAMD (2.14, 3b6,
3b6-CUDA) & VMD 1.9.4a57 worked fantastically well under WSL.

# A few comments for the record
I'm on Windows 11, using WSL-1 with Ubuntu.

VMD required additional libraries:
apt install libgl1-mesa-glx ibxinerama1 libxi6 tcsh

I also exported LD_LIBRARY_PATH to include VMD install
export LD_LIBRARY_PATH=/home/dgomes/software/vmd/lib/:${LD_LIBRARY_PATH}

Friendly,
Diego.

On Mon, Jan 29, 2024 at 10:17 AM Diego Gomes <diego.enry_at_gmail.com> wrote:

> I'll look into the issue, which looks like a Windows-only issue, and I bet
> it is related to a 2Gb file size limitation.
>
> Can you please share which Windows version you are using? Also, did you
> try using NAMD 2.14 instead of 2.13 ?
>
> Friendly,
> Diego.
>
>
> My bet is that 1M is less than 2Gb, and 4M is > 2Gb.
>
> On Fri, Jan 26, 2024 at 8:18 AM Alexei Rossokhin <
> alrossokhin_at_remove_yahoo.com> wrote:
>
>> Dear VMD users,
>> recently installed VMD for WIN64 version 1.9.4a53 (June 29, 2021). It
>> reads my large DCD files correctly. I can visualize trajectories
>> assembled from individual files with a total of over 4M iterations for a
>> system with 161778 atoms.
>> However, when I use the NAMDenergy plugin, I can only calculate energy
>> for runs with 1M iterations. If I upload more, I will get an error. In
>> the log file:
>>
>> dcdplugin) Could not access file 'namd-temp.dcd'.
>> TCL: coorfile: Error opening file namd-temp.dcd
>> FATAL ERROR: coorfile: Error opening file namd-temp.dcd
>> while executing
>> "coorfile open dcd namd-temp.dcd"
>> (file "namd-temp.namd" line 36)
>>
>>
>> It appears when the following command runs
>> F:/NAMD_2.13_Win64-multicore/namd2.exe namd-temp.namd
>>
>> If anyone has encountered this problem before, I would appreciate any
>> advice.
>>
>> Alexey
>>
>
>
> --
> Diego Enry B. Gomes, PhD
> Department of Physics at Auburn University &
> NIH Center for Macromolecular Modeling and Visualization
> Leach Science Center - Ste. 3182 - Auburn, AL
> dgomes_at_auburn.edu
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu