[gmx-users] QMMM with GROMACS and DFTB3

Hello everyone, I was wondering if GROMACS 2016(or 2018) can be interfaced with any QM program like GAMESS-US or ORCA. So far from my searches I found out that it can be done using GROMACS version 5 and DFTB3 according to this website:

Re: [gmx-users] cudaMallocHost filed: unknown error

As a side-note, your mdrun invocation does not seem suitable for GPU accelerated runs, you'd most likely be better of running fewer ranks. -- Szilárd On Fri, Mar 23, 2018 at 9:26 PM, Christopher Neale wrote: > Hello, > > I am running gromacs 5.1.2 on single nodes

Re: [gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??

rlist >= rcoulomb / rvdw is the correct one, the list cutoff has to be at least as long as the longest of the interaction cut-offs. -- Szilárd On Mon, Mar 26, 2018 at 1:05 PM, huolei peng wrote: > In the user guide of Gromacs 2016 (or 2018), it shows " rlist>=rcoulomb " >

Re: [gmx-users] What's new in GROMACS 2018? - a BioExcel webinar

Hi again, We just realized there was a mistake on the website, and the *webinar is scheduled for 13:00 BST (UK) / 14:00 CEST time.* The GoToWebinar platform, where you register, has the correct time. Rossen On 2018-03-26 11:25, Rossen Apostolov wrote: Dear GROMACS users, BioExcel CoE

Re: [gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?

On 3/26/18 8:01 AM, ZHANG Cheng wrote: Dear Gromacs, I use Command line: gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns and was told: Error in user input: Invalid command-line options Unknown command-line option -tu So why "gyrate" could not be supplied

[gmx-users] why "gmx gyrate" could not be supplied with "-tu ns" option?

Dear Gromacs, I use Command line: gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns and was told: Error in user input: Invalid command-line options Unknown command-line option -tu So why "gyrate" could not be supplied with "-tu ns" option? Thank you. Yours

[gmx-users] Confusions about rlist>=rcoulomb and rlist>=rvdw in the mdp options in Gromacs 2016 (or 2018) user guide??

In the user guide of Gromacs 2016 (or 2018), it shows " rlist>=rcoulomb " or "rlist>=rvdw" in several places (see the links below), which are in contrast to those in version of 5.15. Are those changes due to typos? Thanks.

[gmx-users] Periodicity in umbrella sampling

Hi to everyone, I am performing an umbrella sampling simulation of an ion pulled through a biphasic system. The box is 3.6 X 3.6 X 7.3 nm and the ion has been pulled along the z-axys for about 3 nm. In Justin Lemkul's tutorial about umbrella sampling

[gmx-users] What's new in GROMACS 2018? - a BioExcel webinar

Dear GROMACS users, BioExcel CoE (https://bioexcel.eu) is organizing *tomorrow from 14:00 GMT (15:00 CEST) *a webinar on the features, hardware support and various enhancements in the latest 2018 major release. At the end of the presentation, Mark Abraham, the GROMACS development manager,