# \#computational-chemistry **URL:** https://ask.cyberinfrastructure.org/tag/computational-chemistry/69.md [Latest](https://ask.cyberinfrastructure.org/latest.md) · [Categories](https://ask.cyberinfrastructure.org/categories.md) · [Tags](https://ask.cyberinfrastructure.org/tags.md) --- ## [Error while constraining angle in gromacs](https://ask.cyberinfrastructure.org/t/error-while-constraining-angle-in-gromacs/2922)
**Author:** [@anupama\_sharma](https://ask.cyberinfrastructure.org/u/anupama_sharma)\ **Replies:** 1\ **Last updated:** [August 25, 2023, 4:16pm UTC](https://ask.cyberinfrastructure.org/t/error-while-constraining-angle-in-gromacs/2922 "2023-08-25T16:16:51Z")
I am trying to simulate dimethyl -ether molecule constraining all bonds and angles. I am using lincs constraint solver with constraint = all-angles in \*.mdp file for simulation in gromacs. But I ended up with errors. "… --- ## [WebMo alternatives](https://ask.cyberinfrastructure.org/t/webmo-alternatives/2018)
**Author:** [@jeff.ohrstrom](https://ask.cyberinfrastructure.org/u/jeff.ohrstrom)\ **Replies:** 3\ **Last updated:** [June 19, 2023, 8:39pm UTC](https://ask.cyberinfrastructure.org/t/webmo-alternatives/2018 "2023-06-19T20:39:44Z")
I’m finding it increasingly difficult to manage our WebMo deployment. We have all sorts of little hacks to get it to work with our systems (it doesn’t support Slurm well - we had to add a hack for --time flag through the… --- ## [Rutgers University is hiring a Director of Research Support!](https://ask.cyberinfrastructure.org/t/rutgers-university-is-hiring-a-director-of-research-support/2713)
**Author:** [@JanaeBaker](https://ask.cyberinfrastructure.org/u/JanaeBaker)\ **Replies:** 0\ **Last updated:** [March 20, 2023, 10:06pm UTC](https://ask.cyberinfrastructure.org/t/rutgers-university-is-hiring-a-director-of-research-support/2713 "2023-03-20T22:06:36Z")
The Rutgers’ Office of Advanced Research Computing (OARC) is on the look for a Director of Research Support to join our growing team! Rutgers is a leading national research university and the State of New Jersey’s preem… --- ## [Running COMSOL with MATLAB using LiveLink on SLURM cluster](https://ask.cyberinfrastructure.org/t/running-comsol-with-matlab-using-livelink-on-slurm-cluster/281)
**Author:** [@toreliza](https://ask.cyberinfrastructure.org/u/toreliza)\ **Replies:** 0\ **Last updated:** [July 12, 2018, 10:25pm UTC](https://ask.cyberinfrastructure.org/t/running-comsol-with-matlab-using-livelink-on-slurm-cluster/281 "2018-07-12T22:25:25Z")
A few years ago, I was working with a researcher trying to run a calculation in Matlab while executing a job in COMSOL, and to use the results of the Matlab calculation in the running COMSOL job. Much effort was put int… --- ## [Postdoc position in](https://ask.cyberinfrastructure.org/t/postdoc-position-in/2439)
**Author:** [@molpm](https://ask.cyberinfrastructure.org/u/molpm)\ **Replies:** 0\ **Last updated:** [August 3, 2022, 10:19am UTC](https://ask.cyberinfrastructure.org/t/postdoc-position-in/2439 "2022-08-03T10:19:11Z")
A postdoctoral position is offered in the Department of Chemistry at Universidad Autonoma de Madrid (Madrid, Spain) to work in the development of an expert system to predict the environmental impact of pesticides based i… --- ## [Research assitant position at UAM, Madrid (ES)](https://ask.cyberinfrastructure.org/t/research-assitant-position-at-uam-madrid-es/2438)
**Author:** [@molpm](https://ask.cyberinfrastructure.org/u/molpm)\ **Replies:** 0\ **Last updated:** [August 3, 2022, 10:03am UTC](https://ask.cyberinfrastructure.org/t/research-assitant-position-at-uam-madrid-es/2438 "2022-08-03T10:03:50Z")
A research assistant position (predoctoral level) is offered in the Department of Chemistry at Universidad Autonoma de Madrid (Madrid, Spain) to work in the generation of a database of Quantum Chemistry calculations of p… --- ## [How many processors and how much memory should I request for a Gaussian calculation?](https://ask.cyberinfrastructure.org/t/how-many-processors-and-how-much-memory-should-i-request-for-a-gaussian-calculation/232)
**Author:** [@ncolella](https://ask.cyberinfrastructure.org/u/ncolella)\ **Replies:** 4\ **Last updated:** [May 21, 2021, 12:09am UTC](https://ask.cyberinfrastructure.org/t/how-many-processors-and-how-much-memory-should-i-request-for-a-gaussian-calculation/232 "2021-05-21T00:09:12Z")
How many resources should I allocate for a typical Gaussian calculation? How do I assign them? --- ## [When using a GPU to accelerate NAMD, what are the drawbacks of using a single-precision GPU?](https://ask.cyberinfrastructure.org/t/when-using-a-gpu-to-accelerate-namd-what-are-the-drawbacks-of-using-a-single-precision-gpu/1429)
**Author:** [@jgoodhue](https://ask.cyberinfrastructure.org/u/jgoodhue)\ **Replies:** 2\ **Last updated:** [July 27, 2020, 7:57pm UTC](https://ask.cyberinfrastructure.org/t/when-using-a-gpu-to-accelerate-namd-what-are-the-drawbacks-of-using-a-single-precision-gpu/1429 "2020-07-27T19:57:27Z")
I see that NAMD has versions for both double precision and single precision GPUs. Single-precision GPUs are attractive because they are less expensive. Can someone say how the lower precision would affect the quality o… --- ## [Implementing full geometry constraints in GROMACS simulations](https://ask.cyberinfrastructure.org/t/implementing-full-geometry-constraints-in-gromacs-simulations/934)
**Author:** [@RyanRogers](https://ask.cyberinfrastructure.org/u/RyanRogers)\ **Replies:** 3\ **Last updated:** [June 18, 2019, 10:17pm UTC](https://ask.cyberinfrastructure.org/t/implementing-full-geometry-constraints-in-gromacs-simulations/934 "2019-06-18T22:17:40Z")
Does anyone have experience with molecular dynamics simulations in GROMACS with geometry constraints? I know that GROMACS implements LINCS, SHAKE, and SETTLE, in order to constrain chemical bond lengths, angles, etc., an… --- ## [What is GAMESS?](https://ask.cyberinfrastructure.org/t/what-is-gamess/662)
**Author:** [@vsoch](https://ask.cyberinfrastructure.org/u/vsoch)\ **Replies:** 3\ **Last updated:** [May 11, 2019, 1:26am UTC](https://ask.cyberinfrastructure.org/t/what-is-gamess/662 "2019-05-11T01:26:27Z")
There is a long list of questions that are asking about something called GAMESS, for example: Is there a way to reduce the amount of disk files GAMESS uses, or even run the calculations entirely in RAM? Does GAMESS ben… --- ## [Does GAMESS benefit from running calculations on multiple compute nodes? If so, what methods scale the best across many compute nodes on a cluster?](https://ask.cyberinfrastructure.org/t/does-gamess-benefit-from-running-calculations-on-multiple-compute-nodes-if-so-what-methods-scale-the-best-across-many-compute-nodes-on-a-cluster/262)
**Author:** [@srpruitt](https://ask.cyberinfrastructure.org/u/srpruitt)\ **Replies:** 2\ **Last updated:** [July 25, 2018, 12:09pm UTC](https://ask.cyberinfrastructure.org/t/does-gamess-benefit-from-running-calculations-on-multiple-compute-nodes-if-so-what-methods-scale-the-best-across-many-compute-nodes-on-a-cluster/262 "2018-07-25T12:09:39Z")
Some of my calculations are taking a long time to run on a single compute node, and I would like to speed them up as much as possible. I am also willing to use semi-empirical methods such as DFT, or even a fragmentation… --- ## [How many MPI ranks should I request for a GAMESS calculation?](https://ask.cyberinfrastructure.org/t/how-many-mpi-ranks-should-i-request-for-a-gamess-calculation/260)
**Author:** [@srpruitt](https://ask.cyberinfrastructure.org/u/srpruitt)\ **Replies:** 1\ **Last updated:** [July 24, 2018, 4:30pm UTC](https://ask.cyberinfrastructure.org/t/how-many-mpi-ranks-should-i-request-for-a-gamess-calculation/260 "2018-07-24T16:30:33Z")
Specifically, I am trying to figure out the optimal number of processes to scale my MP2 calculation, while still having enough RAM available per process. --- ## [How can I restart my GAMESS calculation and resubmit?](https://ask.cyberinfrastructure.org/t/how-can-i-restart-my-gamess-calculation-and-resubmit/259)
**Author:** [@srpruitt](https://ask.cyberinfrastructure.org/u/srpruitt)\ **Replies:** 1\ **Last updated:** [July 24, 2018, 4:26pm UTC](https://ask.cyberinfrastructure.org/t/how-can-i-restart-my-gamess-calculation-and-resubmit/259 "2018-07-24T16:26:06Z")
My GAMESS geometry optimization did not converge before my hitting my wall time limit. Instead of restarting all the time, I would like to try and string together a series of optimizations together to increase my job th… --- ## [Is there a way to reduce the amount of disk files GAMESS uses, or even run the calculations entirely in RAM?](https://ask.cyberinfrastructure.org/t/is-there-a-way-to-reduce-the-amount-of-disk-files-gamess-uses-or-even-run-the-calculations-entirely-in-ram/261)
**Author:** [@srpruitt](https://ask.cyberinfrastructure.org/u/srpruitt)\ **Replies:** 1\ **Last updated:** [July 24, 2018, 4:20pm UTC](https://ask.cyberinfrastructure.org/t/is-there-a-way-to-reduce-the-amount-of-disk-files-gamess-uses-or-even-run-the-calculations-entirely-in-ram/261 "2018-07-24T16:20:28Z")
GAMESS has a long list of files it uses during a calculation, but my local cluster has very slow local disks. Even worse, the system I am using remotely has no local disks on the compute node and I have to use the remot… --- ## [How can I determine how much memory I need before submitting my GAMESS calculation?](https://ask.cyberinfrastructure.org/t/how-can-i-determine-how-much-memory-i-need-before-submitting-my-gamess-calculation/258)
**Author:** [@srpruitt](https://ask.cyberinfrastructure.org/u/srpruitt)\ **Replies:** 1\ **Last updated:** [July 24, 2018, 4:07pm UTC](https://ask.cyberinfrastructure.org/t/how-can-i-determine-how-much-memory-i-need-before-submitting-my-gamess-calculation/258 "2018-07-24T16:07:33Z")
Some of my large GAMESS calculations are failing due to insufficient memory after waiting in the queue for days. I’d like to calculate the amount of memory I need before submitting so I can be sure my jobs don’t fail. --- ## [How can I run Gaussian09 on a server?](https://ask.cyberinfrastructure.org/t/how-can-i-run-gaussian09-on-a-server/233)
**Author:** [@ncolella](https://ask.cyberinfrastructure.org/u/ncolella)\ **Replies:** 1\ **Last updated:** [June 12, 2018, 9:19pm UTC](https://ask.cyberinfrastructure.org/t/how-can-i-run-gaussian09-on-a-server/233 "2018-06-12T21:19:00Z")
What files do I need to run Gaussian on a compute node?