[gmx-users] Ris: compatibility between ff14SB and GLYCAM_06j-1 force field

Inviato dal mio dispositivo mobile Huawei Dear Louise, Did you check if the lipids you need are available with lipid17 force field? It is an Amber - based one and it is compatible with ff14SB. Notably, it has the same scaling factors of ff14SB. Hope this helps, Tommaso Messaggio

[gmx-users] compatibility between ff14SB and GLYCAM_06j-1 force field

Hello, I get a compatibility error between ff14SB and GLYCAM_06j-1 with gromacs 2018.4. I prepared my model (protein with co factors and lipids) via tleap and when I tried to convert to gromacs file with ParmEd I got this error: "Structure has mixed 1-4 scaling which is not supported by

Re: [gmx-users] dssp error

I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an executable Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao escreveu: > Have a check the installation of DSSP, > did you set the variable DSSP for do_dssp? > > > All the best, > Qinghua > > > On 3/21/19 8:01 PM, Mario

Re: [gmx-users] dssp error

Have a check the installation of DSSP, did you set the variable DSSP for do_dssp? All the best, Qinghua On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp,

Re: [gmx-users] dssp error

gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option.

Re: [gmx-users] dssp error

Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run

[gmx-users] dssp error

Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program:

Re: [gmx-users] Freezing structure's atom

There a "gmx make_ndx" command to make .ndx group. They ahve their names. And it needs to be inserted in there. Please have a look at the .ndx file to see what it does. For any name it's just a list of atoms. On Thu, 21 Mar 2019 at 14:39, Hadi Rahmaninejad wrote: > Sorry I forgot to ask this

Re: [gmx-users] Freezing structure's atom

Sorry I forgot to ask this question: did you determine "slab" group in your .gro file? On Thu, Mar 21, 2019 at 10:29 AM Hadi Rahmaninejad wrote: > Hello Mateusz, > > Thank you for your help. However, still I am a little confused. suppose > that this is the .mdp file for minimization: >

Re: [gmx-users] Freezing structure's atom

Hello Mateusz, Thank you for your help. However, still I am a little confused. suppose that this is the .mdp file for minimization: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0

Re: [gmx-users] Freezing structure's atom

Hi Hadi, You can freeze atoms in any simulation, so yes in nvt.mdp or any other .mdp. That is also why the freezegrps in the URL I attached is in the section called mdp-options. When you run grompp to create the .tpr run file, it will not recognize the group "slab" so you will have to give it