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uhoh
uhoh
1:57 AM
28
Q: Why aren't Runge-Kutta methods used for molecular dynamics simulations?

WedgeAntillesOne of the most used schemes for solving ordinary differential equations numerically is the fourth-order Runge-Kutta method. Why isn't it used to integrate the equation of motion of particles in molecular dynamics?

statistical-mechanics integration simulations differential-equations molecular-dynamics
 
 
7 hours later…
r/comp_chem
r/comp_chem
9:11 AM
Computational Chemistry: Pulling a box in X-direction at a constant rate for calculating Young's Modulus of a solid in Gro…
posted on May 12, 2022 by /u/roshan2004

Hi, I am currently trying to pull a box in X-direction with these settings in my mdp file of gromacs tcoupl = v-rescale tc-grps = System tau_t = 1.0 ref_t = 310 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422 compressibility = 0 3e-4 ref_p = 1 1 gen_vel = no gen_temp = 310 gen_seed = 473529 ; options for def…

 
Feeds
Feeds
9:28 AM
0
Q: How to run SCRF in Gaussian with extra basis?

ggerezI want to run a SCRF calculation in Gaussian for a molecule. This has been done as standard with several geometries without issue using the aug-cc-pvtz basis and the externaliteration keyword. I've run into an issue when attempting to run Iodine, as the basis i chose does not include it. I've tri...

computational-chemistry solutions software
 
 
6 hours later…
r/comp_chem
r/comp_chem
3:56 PM
Computational Chemistry: Adsorption in ORCA
posted on May 12, 2022 by /u/Lucky-Technology-547

Hello! I need help regarding my thesis about adsorption. I have so many questions nut first, do I need to replace one of the atoms in my molecular system with a metal (example is the hydrogen in the carboxylic acid group with a Pb atom) or I just add a metal atom adjacent to the molecule, then run the code using ORCA? thanks. submitted by /u/Lucky-Technology-547 [link] …

 
 
3 hours later…
r/comp_chem
r/comp_chem
6:29 PM
Computational Chemistry: Plotting & Visualizing molecular and periodic MOs and Densities using TURBOMOLE
posted on May 12, 2022 by /u/manassharma007

https://www.youtube.com/watch?v=549bXQvaAjU&t=52s submitted by /u/manassharma007 [link] [comments]

 
 
4 hours later…
r/comp_chem
r/comp_chem
10:17 PM
Computational Chemistry: Understanding Orca error when running in parallel
posted on May 12, 2022 by /u/learner_254

I get the following error when I run with parallel: An error occurred in MPI_Type_match_size reported by process [4120707073,1] on communicator MPI_COMM_WORLD MPI_ERR_ARG: invalid argument of some other kind MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198 6 more proces…

 

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