Re: [gmx-users] disulfide bridges

Oh thank you so much, I did not know it was a reference value. Given a range of values might exist in one system I'm guessing minimization would be the only way to deal with such a situation. Best, Miro On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote: > > > On 5/2/20 6:54 AM, Mi

[gmx-users] disulfide bridges

Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. Any way I can nudge it in the right direction without

[gmx-users] debugging

Hi all, I am interested in how Gromacs works at the back end but I don't have much C experience so this might be silly. I have noticed that one of my systems that includes virtual sites parses fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a segmentation fault. 21169

Re: [gmx-users] semiisotropic pressure coupling.

Incredible thank you. On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, wrote: > > > On 4/14/20 10:12 PM, Miro Astore wrote: > > Hello all, > > > > I am working with a rather large membrane bound protein. I was getting > > an issue awhile ago where if the pro

[gmx-users] semiisotropic pressure coupling.

Hello all, I am working with a rather large membrane bound protein. I was getting an issue awhile ago where if the protein moved to the edge of the box the box would elongate in the z direction. I fixed this in the short term by setting my xy compressibility to 0 in my production mdp file pcoupl

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

- Best, Miro On Tue, Mar 31, 2020 at 9:58 AM Szilárd Páll wrote: > > 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 wit

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

. I will soon see if i can get away with fewer replicas. Thanks for your help. Miro On Sun, Mar 29, 2020 at 9:04 PM Benson Muite wrote: > > > On Sun, Mar 29, 2020, at 4:55 AM, Miro Astore wrote: > > Hi everybody. I've been experimenting with REMD for my system running > > on

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

correction: 99.3% is going into NxN Ewald Elec. + LJ [F] On Sun, Mar 29, 2020 at 12:55 PM 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 compli

[gmx-users] replica exchange simulations performance issues.

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). My run configuration is mpirun -np 4 --map-by numa gmx_mpi

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

I have something like this on my github. https://github.com/Miro-Astore/gromacs_scripts/tree/master/pbs_files/gadi File is memb0.pbs let me know if you have any questions. On Sat., 15 Feb. 2020, 8:45 am Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello grom

Re: [gmx-users] misunderstanding comm-grps

Oh thank you very much I think I got confused looking at older documentation. What sort of artefacts get created by using comm-grps = Protein non-Protein? On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: > > > > On 2/3/20 7:33 PM, Miro Astore wrote: > > Hi everyone, &g

[gmx-users] misunderstanding comm-grps

Hi everyone, I have tried using comm_grps to try and remove center of mass motion from my system. I used the following configuration comm_grps = non-Protein Protein nstcomm = 100 comm_mode = linear comm_grps = non-Protein Protein

Re: [gmx-users] Charmm to Gromacs itps

Would topotools in vmd not work in this context? I haven't used it but read about it recently and it would seem this is the use case. Of course you also need parameters. Wondering. Best, Miro Le sam. 1 févr. 2020 à 00:55, Justin Lemkul a écrit : > > > On 1/31/20 8:25 AM, atb files wrote: > > >

[gmx-users] constant x-y plane area for membrane simulations.

Hello all, I'm just wondering if gromacs supports constant x-y plane area for npt simulations like NAMD does. Best, Miro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] trjcat and trjconv performance

Hello all. I need to use trjcat and trjconv often and I am wondering if there is any way to speed up these utilities. They seem quite slow at the moment compared to the catdcd binary in the vmd distribution. Best, Miro -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] learning gromacs

Hi, I'm new to gromacs myself. Your best bet if you're new to Molecular dynamics is to do some tutorials and read best practices to try and understand what the computer is actually doing and why. http://www.mdtutorials.com/gmx/ I would recommend starting with the lysozyme in water tutorial as it

Re: [gmx-users] top2psf license

and secondary structures without the need for such a script, directly reading itp files. Even being able to determine secondary structures from martini. https://twitter.com/Matth_Chavent/status/1145727900286693376 Best, Miro Le mer. 22 janv. 2020 à 20:07, Miro Astore a écrit : > Does anyone k

[gmx-users] top2psf license

Does anyone know what the license is for the top2psf.pl script. I'd like to modify and distribute it if possible. Best, Miro. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Loading topology into vmd

at is not the most elegant way, but it works in my case. > For more elegant ways, you could ask to VMD maillist. > Best regards > Alessandra > > > On Tue, Jan 14, 2020 at 8:59 PM Miro Astore wrote: > > > Hi kenny, thanks for getting back to me. > > > > I use somethin

Re: [gmx-users] Loading topology into vmd

acs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore < > miro.ast...@gmail.com> > Verzonden: dinsdag 14 januari 2020 3:48 > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se

[gmx-users] Loading topology into vmd

Hello all, I'm just wondering how people load topologies for systems simulated in gromacs into vmd. It is very annoying to have bonds that aren't in the simulation placed in the visualisation. I'm wondering if anyone has a solution that is easier than simply creating a psf file of the .gro system

[gmx-users] conveniently placing restraints on a subset of a molecule

Hello, I am new to the gromacs work flow, I come from using NAMD. An example of what I want to do is place harmonic restraints on a subset of a molecule, for example all of the CA atoms in a protein backbone. I have found the genrestr function which I would have expected would do the trick.