VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Wed Sep 10 2025 - 09:06:12 CDT

Hi Josh thank you for your kind update:) and yes I have moved to the NSF
Cluster and modified the method (RI) and Basis Set to reduce the
time/resource requirements;
the below modification seems that it will possibly generate final results
in a satisfactory amount of time, thank you again for your reply:), Joel 🚀

 ! MP2 6-31G* Tight SCF opt NumFreq to ! RI-MP2 6-31G* def2/J def2-SVP/C
TightSCF Opt NumFreq

On Wed, Sep 10, 2025 at 3:33 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:

> Hi Joel,
>
> QM does not scale very well. The complexity of the computation grows
> polynomially with the number of atoms, something like O(N^7) if I remember
> correctly. So if you know how long a 32 atom ligand would take for this
> calculation, your bigger ligand would take 128x longer. This is of course
> not great, but I've parameterized lignin dimers before, and those are only
> a little smaller (~50 atoms), so 64 atoms is actually not that bad if you
> just want a charge distribution.
>
> However, looking at my logs, I only did charge optimization for those big
> ones, using the monomers (which only had ~25-30 atoms) to do the expensive
> dihedral scans and hessian calculations. On hardware I had available, that
> took less than 2 days (the longest I see quickly is 1 day 17 hours). So,
> even if everything is *perfect*, on a system twice as big I'd expect this
> to run full blast for 256 days, or about 8.4 months. In the best case
> scenario, I might be too pessimistic in my timings, since I did this when I
> was a postdoc and CPUs have gotten more capable since then, and you'd only
> need to wait another 3 months for an answer. But you'll likely also want to
> do dihedral scans, which are just as expensive, so you may be better off
> with another approach entirely.
>
> -Josh
>
> On 7/11/25 1:29 PM, Joel Subach wrote:
>
> Hell Forum,
>
> I am running the command:
>
> orca 14C.hess.inp > 14C.hess.output.out
>
> to generate the output.out file towards the subsequent generation of Bond
> and Angle
> optimized reparametrization due to CGenFF penalty scores, the aim is
> towards Gromacs Protein-Ligand Complex Analysis.
>
> I am running the above command in the NSF Cluster exhibiting the below
> specs,
> how long should this execution take to generate final results for a ligand
> of 64-atoms? (The above was executed almost three-months ago and is still
> running successfully without final results yet, maybe the delay is due to a
> sharing of this NSF Cluster.)
>
> Attribute Kentucky Research Informatics Cloud (KyRIC) Large Memory Nodes
> *Nodes* 5
> *CPU Type* Broadwell class
> *CPU Speed* 2 Ghz
> *CPU Cores per Node* 40
> *RAM per CPU Core* 75 GB
> *GPU* None
> *Local Storage per Node* 6,000 GB
>
>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityvermaaslab.github.io
>
>

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