[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

Hi, I am using gromacs-2019.4. I have been running simulations box that contains a peptide embedded in a DOPC bilayer membrane, using all atom simulations. I have been running for weeks in a TACC computer that has 4 gpu in a single node, so I usually run 4 trajectories in a single node using

Re: [gmx-users] Script for looping n simulations

On 3/10/20 3:20 PM, Neena Susan Eappen wrote: Hi Justin, I tried that script out, but I want the output in a different way. So I have n log files (.log), and I want to extract potential energy value say from line x from all n log files. Is there a way I can export all these potential

Re: [gmx-users] Script for looping n simulations

Hi Justin, I tried that script out, but I want the output in a different way. So I have n log files (.log), and I want to extract potential energy value say from line x from all n log files. Is there a way I can export all these potential energy values into one text file with one script? Many

Re: [gmx-users] [gmx-developers] The setup of gpu_id has a bug?

Hi, Please sue the user's mailing list for questions not related to GROMACS development. By default. the "-gpu_id" option takes a sequence of digits corresponding to the numeric identifiers of GPUs. In cases where there are >10 GPUs in a system, a comma-separated string should be used, see

Re: [gmx-users] Replicate a structure

> Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o > new_system.gro right?? Based on what you described, I'd say that's correct. Try it out and then visualize the resulting .gro file to see if things are how you want them to be. > > On Tue, Mar 10, 2020, 6:01 PM John Whittaker <

Re: [gmx-users] Replicate a structure

Then my command would be gmx genconf -f system.gro -nbox 2 1 1 -o new_system.gro right?? On Tue, Mar 10, 2020, 6:01 PM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > Probably better to use gmx genconf; This situation is probably its main > purpose. > > - John > > > Gmx editconf you

Re: [gmx-users] Replicate a structure

Probably better to use gmx genconf; This situation is probably its main purpose. - John > Gmx editconf you can use with -translate flag...after that merz the > coordinates of two water droplets. I hope this may help you. > > On Tue 10 Mar, 2020, 9:35 AM Devargya Chakraborty, < >

Re: [gmx-users] Clarification on the "-surface" and "-output" options of "gmx sasa"

On Mon, Mar 9, 2020 at 2:47 PM ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > > > There seems to be very little explanation on the "-surface" and "-output" > options of "gmx sasa": > -surface: This should always consist of all non-solvent atoms in the > system. The area of this group is

Re: [gmx-users] Setting a electric field in a simulation

Den 2020-03-10 kl. 03:17, skrev Mijiddorj B: Dear GMX users, I would like to perform MD simulations of solutions applying electric fields such as the microwave heating process. Is it possible to perform in gromacs? 1. How can I set the external electric field in the simulations? (from the