[CP2K-user] [CP2K:18570] Re: Request for assistance with MD simulation

captain mus captainmozak at gmail.com
Tue Mar 21 15:12:54 UTC 2023

Hi Xiao Peng

If you asking about the update (eg, md output, vel, pos, or restart) then 
you have to take care about the PRINT section. From what I'm seeing in your 
input, you set print for MD EACH but then you put 0 as the value something 
like this 
        MD     0 #Output frequency of velocities, 0 means never
      &END EACH

I mean if you don't want to print the velocities then just disable it 
(e.g., with ! of #), but if you want to print it lets say each MD step then 
you just set something like this 

    FILENAME = velocity.xyz

This also the same with the trajectory,, forces or restart, you can find 
the details here  https://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/PRINT.html

one more thing, in you script file, please set the execution with -o 
out.out (or what ever output file you want to name) so you can check the 
properties of your system related to the calculation in that out.out file. 
I hope this help

On Monday, March 20, 2023 at 7:41:53 AM UTC+1 xiao peng wrote:

> Dear All,
> I am writing to seek your expertise in a computational chemistry problem 
> that I have been encountering. I am using the cp2k.popt version of the cp2k 
> program and the Multiwfn software to generate an input file (cp2k.inp) for 
> a molecular dynamics (MD) simulation. The simulation is performed using 
> the NPT_F ensemble and is run on a cluster with 64 cores using mpirun.
> Unfortunately, the MD simulation stops updating after approximately 5 
> steps, while the CPU remains occupied. The cluster has dual AMD 7763 CPUs 
> and 512 GB of memory, which should be sufficient for the simulation. 
> However, I have observed that the simulation does not report any errors or 
> warnings in the output file, and the memory usage does not exceed 40 GB.
> I have also attempted to troubleshoot the issue by testing different 
> settings such as thermostats (Nose, CSVR), orbital transformation (OT) or 
> diagonalization, including DFTD3 dispersion correction, and trying 
> different pseudopotentials and basis sets, but these have not improved the 
> simulation.
> I am unsure what the issue may be and would greatly appreciate any insight 
> or advice you could provide on how to resolve this problem. Thank you for 
> your time and consideration.
> Best regards,
> Peng Xiao

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