[gmx-users] Glycosylation of ASN

Hi, Have you tried reducing the timestep in mdp? Yes, I tried. But no hope. On Mon, May 4, 2020, 2:52 AM Naba https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> wrote: >* Dear users and developers, *>>* I have spent extensive amount of time to model glycosylated ASN residues

[gmx-users] apply protonation state CYS amino acid

Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS Thanks -- Gromacs Users mailing list * Please

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

1/ it means that between the original coordinate file loaded with vmd and the frame you are looking at there from the trajectory file, those atoms have moved across the periodic boundary and vmd is still drawing the bond between them. vmd knows nothing about bonds, it guesses where the bonds

Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

Hi Jochen, Thank you for the suggestions. Best, Zheng On Mon, May 4, 2020 at 5:24 PM Jochen Hub wrote: > > > Am 04.05.20 um 23:21 schrieb Jochen Hub: > > > > > > Am 04.05.20 um 21:33 schrieb Zheng Ruan: > >> Hi, > >> > >> I'm trying to setup an antiparallel membrane system for CompEL > >>

Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

Am 04.05.20 um 23:21 schrieb Jochen Hub: Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f

Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro

[gmx-users] Set up anti parallel membrane system for CompEL simulation

Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one

Re: [gmx-users] GROMACS mailing-list will move to a forum

Hello again @ all gmx-users! A month has passed and we have moved forward with our work to move the user mailing list to the [discussion forum] https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8 May 2020. We are now ready to accept people signing up to the forum at

[gmx-users] Free energy calculation and Lincs warning

Dear Gromacs users I am doing free energy calculation of the protein-ligand system in gromacs 2020 in which I am annihilating ligand by removing charges and vdw interactions. During Vdw removal I am facing lincs warning and my system crashes by generating different pdb structures. I have tried to

[gmx-users] Need help creating md.mdp for silica(quartz)?

I have done simulation water in nanopore based on quartz (I use model ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is a link to the pictures at the initial time (1.png) and in the modeling process.

Re: [gmx-users] Plumed tutorial

Hi Dinesh and others, I see a few PLUMED tutorials available online, but I wanted to just let anyone know that if they have developed a PLUMED tutorial or are working to create a new one, please feel free to submit any high-quality tutorials to LiveCoMS Journal: https://www.livecomsjournal.org/

[gmx-users] Plumed tutorial

Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED patch.I would like to know if there is a step-by-step tutorial that could help run metadynamics simulations using PLUMED (like the Gromacs tutorials already available) Dinesh Kumar -- Gromacs Users mailing list *

Re: [gmx-users] dssp 3.1.4

Hi, Do check out gmx do_dssp -h and make sure your dssp binary is the right version, with executable permissions, in the right place (or alternatively the appropriate environment variable is set, so that do_dssp can find dssp) Mark On Fri, 1 May 2020 at 18:47, Iman Katouzian wrote: > Good

[gmx-users] How to recover the corrupted .xtc file?

Dear users, I have a corrupted .xtc file. I can read only part of the whole frame in VMD. When I gmx check the .edr file, there is no problem with 5001 frames. However if I do gmx check the .xtc file, then I get only 2954 frames out of 50001 frames. I used Gromacs 2019.6 with CUDA on a single