[gmx-users] Fwd: Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

> > > Dear Benson and Szilard, > > Thank you for your interest. Benson, I will try to answer you questions > first: > 1) No, I have only tested 2018.3 so far. I just changed from Gromacs 5.1.4 > and these are my first tests. > 2) Not yet but I plan to do it. > 3) The results look reasonable after

Re: [gmx-users] Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

> > Dear Benson and Szilard, > > Thank you for your interest. Benson, I will try to answer you questions > first: > 1) No, I have only tested 2018.3 so far. I just changed from Gromacs 5.1.4 > and these are my first tests. > 2) Not yet but I plan to do it. > 3) The results look reasonable after

Re: [gmx-users] Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

that it is not related to an unstable simulation but only to some kind of software issue. Kind regards, Krzysztof pon., 5 lis 2018 o 21:12 Krzysztof Kolman napisał(a): > Dear Gromacs Users, > > I have problem with my Gromacs 2018.3 that keeps crashing due to > segmentation fault afte

[gmx-users] Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

Dear Gromacs Users, I have problem with my Gromacs 2018.3 that keeps crashing due to segmentation fault after quite long simulations time (more than 12 h wall clock). It is hard for me to tell why because there is no information why, except the segmentation fault message. Please find below

Re: [gmx-users] GMX Error after CUDA update

e, for which the remedy is to recompile. > > Mark > > On Thu, Jun 21, 2018 at 10:54 PM Krzysztof Kolman < > krzysztof.kol...@gmail.com> wrote: > > > Dear Gromacs Users, > > > > After my system update (Manjaro), I can not run Gromacs anymore. I > noticed > &

[gmx-users] GMX Error after CUDA update

Dear Gromacs Users, After my system update (Manjaro), I can not run Gromacs anymore. I noticed that Cuda has been update from version 9.1 to 9.2 and now I get following error: gmx: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory Is

[gmx-users] Gromacs Input Fiels of Interface Forcefield

different interfaces are included in InterfaceFF_1.5 that can be found here: https://bionanostructures.com/interface-md/ The script can be found here (including detailed description how to use it): https://github.com/kolmank/interfaceff2gro I hope you will like it! Best regards, Krzysztof Kolman

Re: [gmx-users] C-formats of forcefield file sections

Dear Justin, Thank you a lot! Best, Krzysztof 2018-04-21 3:26 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/20/18 4:54 PM, Krzysztof Kolman wrote: > >> Dear Gromacs Users, >> >> I am looking for C-formats of sections of force field fil

[gmx-users] C-formats of forcefield file sections

Dear Gromacs Users, I am looking for C-formats of sections of force field files, i.e., [atomtypes], [bondtypes]... In the manual I could only find the C-format of gro file: "%5i%5s%5s%5i%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f". Does someone know where I can find them? Best regards, Krzysztof -- Gromacs

[gmx-users] C-formats of forcefield file sections

Dear Gromacs Users, I am looking for C-formats of sections of force field files, i.e., [atomtypes], [bondtypes]... In the manual I could only find the C-format of gro file: "%5i%5s%5s%5i%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f". Do you know where I can find them? Best regards, Krzysztof -- Gromacs Users

Re: [gmx-users] OPLS3 forcefield

I use and recommend the project STaGE (OPLS-AA and other forcefields): https://gerrit.gromacs.org/#/admin/projects/STaGE Best regards, Krzysztof 2018-04-07 23:04 GMT+02:00 Alex : > Not sure about OPLS3, but for the publicly available OPLS-AA there are > many resources,

Re: [gmx-users] Topology file of molecule

Dear Vytautas and Justin, Thank you both for the help. I will try to perform some dihedral scans of small and simple molecules. Best regards, Krzysztof 2017-12-04 15:24 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 12/4/17 5:31 AM, Krzysztof Kolman wrote: > >>

Re: [gmx-users] Topology file of molecule

ld > be doing in the first place. > > -Justin > > > I hope that helps you. >> >> Best regards, >> >> Magnus >> >> On 2017-11-23 10:24, Krzysztof Kolman wrote: >> >>> Dear Gromacs Users, >>> >>> I would like to perfo

Re: [gmx-users] Topology file of molecule

rameters. Otherwise it is extremely hard to define > what "strange" is in a simulation; you don't know what the molecule should > be doing in the first place. > > -Justin > > > I hope that helps you. >> >> Best regards, >> >> Magnus >> >>

[gmx-users] Topology file of molecule

Dear Gromacs Users, I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created topology files for the silica surface based on the information found in papers describing simulations of quartz (Wensink 2000 -