Re: [gmx-users] Onsager coefficient

Den 2020-03-30 kl. 22:51, skrev Sina Omrani: Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: Hi, I would like to calculate the Onsager coefficient but after months of study, I'm not able

[gmx-users] Generating velocities

Hello everybody, If my molecules are moving and I want to add the velocity, should I generate the velocity through the .mdp file, or should I add the velocities into my .gro file and insert the molecules? Thanks, Mohamed -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] replica exchange simulations performance issues.

I got up to 25-26 ns/day with my 4 replica system (same logic scaled up to 73 replicas) which I think is reasonable. Could I do better? mpirun -np 48 gmx_mpi mdrun -ntomp 1 -v -deffnm memb_prod1 -multidir 1 2 3 4 -replex 1000 I have tried following the manual but I don't think i'm going it

Re: [gmx-users] replica exchange simulations performance issues.

On Sun, Mar 29, 2020 at 3:56 AM Miro Astore wrote: > Hi everybody. I've been experimenting with REMD for my system running > on 48 cores with 4 gpus (I will need to scale up to 73 replicas > because this is a complicated system with many DOF I'm open to being > told this is all a silly idea). >

Re: [gmx-users] Onsager coefficient

Hi dear Gromacs users, Sorry to ask again but I really appreciate the help on this subject. thanks. On Fri, 27 Mar 2020 at 02:23, Sina Omrani wrote: > Hi, I would like to calculate the Onsager coefficient but after months of > study, I'm not able to do that. if anybody can help me I would

[gmx-users] GROMACS - tip7p itp and gro files - couldn't find them anywhere

Hi all, I've seen that recent tip7p water model (https://pubs.acs.org/doi/10.1021/acs.jpcb.9b03149) and wanted to try it out. However, I couldn't find or I missed where the itp and gro files are deposited. Anybody knows where to find them? Thanks a lot in advance! Best, Jacek

[gmx-users] Coupled Gromacs+CP2K QM/MM user survey

Dear Gromacs users, My name is Julien Sindt and I am a member of the BioExcel Centre of Excellence. We aim to provide support to academic and industrial researchers in the use of high-performance computing (HPC) and high-throughput computing (HTC) in biomolecular research (if you're

Re: [gmx-users] GROMACS 2019-rc1 install issues

Also, please don't use Release candidate versions for anything serious. Instead use the latest official release that suits you. Cheers Paul On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote: Hi everyone, I'm a beginner user of GROMACS, and I'm having some troubles with the

Re: [gmx-users] GROMACS 2019-rc1 install issues

Hello, you can't attach files to the list here, either paste the error directly from the terminal or upload the file somewhere and share the link. Cheers Paul On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote: Hi everyone, I'm a beginner user of GROMACS, and I'm having some troubles

Re: [gmx-users] Thin film drifting

Den 2020-03-29 kl. 22:46, skrev Alex: On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel wrote: Den 2020-03-29 kl. 19:43, skrev Alex: Thanks. On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel < sp...@xray.bmc.uu.se> wrote: Den 2020-03-29 kl. 15:16, skrev Alex: Thank Prof. van der

[gmx-users] GROMACS 2019-rc1 install issues

Hi everyone, I'm a beginner user of GROMACS, and I'm having some troubles with the installation. I follow the instruction in http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html , but when i run "make", appear the error shown in file attached. Any advice will be appreciated.

[gmx-users] gmx rdf (Angular Dependence)

Hi, In the 2020.1 Release of Gromacs Documentation, it is written in page 486 the following: "With gmx rdf (page 135) it is also possible to calculate an angle dependent rdf g_AB(r, theta), where the angle theta is defined with respect to a certain laboratory axis e, see Fig. 5.50 B"