GROMACS version: GROMACS modification: Yes/No Here post your question I have used AMber forcefield and tip3p water model to generate protein topology and acpype srver to generate the ligand topoogy, while generating ions.tpr file I am getting error in the .prm file rearding dihedrals : - Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsole…

GROMACS version: gmx22 Hello People, I get want to create the .tpr with my .grofile, to start ab mdrun, however I get an error: invalid pairs type 7 I had to create a residue by my self, so the .itp-file is also self-made. Maybe some of you guys know the solution to that error. Thanks! 1 post - 1 participant Read full topic

GROMACS version: 2020.3 GROMACS modification: No I have two forcefield .itp files. One is given by CHARMGUI membrane builder FF converter from modelling an asymmetric membrane of LPS/POPC. The other is generated from pdb2gmx when I initialised my protein from a pdb file. I am adding my proteins above the membrane, however there is inconsistencies between the forcefields. Using on…

GROMACS version: 2021.4 GROMACS modification: Yes/No Hello, I am facing a problem when running a simulation with a box created with Packmol. My box has 100 molecules of water and I created a topol.top file as: ; Include forcefield parameters #include “oplsaa.ff/forcefield.itp” ; and the SPC/E water model. #include “oplsaa.ff/spce.itp” [ system ] ; Name water [ molecules …

GROMACS version: 2024.1 GROMACS modification: Yes/No Hello, I am attempting to install gromacs 2024.1 patched with plumed 2.9 and apple silicon GPU support. It gets very close to finishing, but crashed out 90% into the gromacs make. It crashes out with the following error (amongst others): /downloads/gromacs-2024.1/src/gromacs/mdrun/md.cpp:308:118: error: use of undeclared id…

GROMACS version: 2024.1 GROMACS modification: No I am trying to implement a GPU driven parallelization of Gromacs in a cloud compute environment using an NVIDIA architecture and I randomly encounter CUDA Error #700 (Or else some other similar data leakage error), the machine type is very large with over 60 gbs of available memory, so I am at a loss for how to approach the problem…

Using gromacs 2022.4 when using IFNDEF_init.top does not produce constrained files, while simply removing them by deleting all “#ifdef FLEXIBLE”, “#else”, “#endif” working_init.top runs correctly. May I ask if i’m doing something wrong with IFDEF, or is gromacs does not read IFDEF correctly ? IFNDEF_init.top (2.1 KB) working_init.top (2.1 KB) 1 post - 1 participant…

GROMACS version: 2024.1 GROMACS modification: Yes/No I’m new posting in the forum, but a long time GROMACS user. I have been working with the colvars module as implemented in GROMACS 2024.1 and am having problems with the “customFunction” command that allows for creating your own collective variables. Below is an example of a very simple colvars.config script that fails with “Er…