Re: [gmx-users] mac OS Catalina segmentation fault

l CMakeConfig file? > > Cheers > > Paul > > On 05/11/2019 21:10, Daskalakis Vangelis wrote: > > Dear all, > > I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have > > successfully compiled several versions of Gromacs (5.1.5, 2018.8, or > > 2019.4) patch

[gmx-users] mac OS Catalina segmentation fault

Dear all, I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have successfully compiled several versions of Gromacs (5.1.5, 2018.8, or 2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019 versions). The compilations are completed without any errors, employing the configu

Re: [gmx-users] soft "exit"

Thank you Mark. That's very helpful Vangelis On Thu, May 11, 2017 at 10:00 AM, Mark Abraham wrote: > Hi, > > On Thu, May 11, 2017 at 8:54 AM Daskalakis Vangelis > wrote: > > > Dear all, > > I am running Gromacs 5.1.4 on a cluster with SLURM workload mana

[gmx-users] soft "exit"

Dear all, I am running Gromacs 5.1.4 on a cluster with SLURM workload manager. How can I terminate the running gromacs jobs (i.e. send the TERM/ INT signals) but also allow time for each job to "soft exit" on the next step ? By "soft exit" I mean that the job should be like it is finished (all the

[gmx-users] from rdf -com to number density

Hello all, I run a simulation (NVT with a large box size) of a TIP4P water cluster which assumes a spherical shape, as expected. I center this sphere in the box throughout the trajectory. I analyze the trajectory with "gmx rdf -com". I choose all waters as both the ref group and the second group. T

Re: [gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

Thank you Justin, Yes, that would do the work. I thought there could be another way, but I won't avoid doing it frame by frame. Thank you again. On Wed, Sep 16, 2015 at 2:55 PM, Justin Lemkul wrote: > > > On 9/15/15 6:13 PM, Daskalakis Vangelis wrote: > >> Hello. >

[gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

Hello. I want to use a dynamic selection scheme (select different atoms based on the same selection criteria for each frame of a trajectory) and pass this selection/ info to the gmx dipoles tool. It seems that the -select option cannot be used. I tried to use dynamic selection through gmx select. T

Re: [gmx-users] Radius of Gyration

k > > > Erik Marklund, PhD > Postdoctoral Research Fellow > Fulford JRF, Somerville College > > Department of Chemistry > Physical & Theoretical Chemistry Laboratory > University of Oxford > South Parks Road > Oxford > OX1 3QZ > > > On 13 Jul 2015, at 11:

Re: [gmx-users] Radius of Gyration

Thank you Peter for your reply. I have tried 'trjconv -pbc cluster -center' before, but despite being so slow (for around 6000 waters), I actually get again some spikes on the Rg due to PBC. I will give it a try again, thank you. On 13/07/15 12:02, Peter Kroon wrote: >* Dear users, *>* I am emp

[gmx-users] Radius of Gyration

Dear users, I am employing gromacs 5.05 to simulate a water cluster (spherical shape) forming on some salt in PBC (NVT). I want to calculate the Radius of Gyration (Rg, through g_gyrate) throughout the simulation time. I have a forming water (spherical) cluster, but due to PBC this spherically shap