GROMACS version: 2021.3 GROMACS modification: No Hi, I generated a new topology on the CGenFF server to use with the CHARMM36 forcefield (most recent version of each was used). I’ve been able to build my system fine, but I got the following error when running grompp prior to energy minimisation: ERROR 1 [file topol.top, line 393]: No default Proper Dih. types The corresponding…

GROMACS version: 2021 GROMACS modification: No Hi, I am trying to run some free energy simulations using GROMACS-2021 but I always get the fatal error below. It seems that this is a bug. Do you know which latter version is stable for free energy calculations? Fatal error: There are 7 perturbed non-bonded pair interactions beyond the pair-list cutoff of 1.26 nm, which is not s…

GROMACS version: 2022.3 GROMACS modification: No Hi, I tried to generate .gro and .top files from a pdb that was prepared for simulation by Schrodinger’s protein preparation wizard. It’s a single chain molecule of calmodulin (PDB ID 2v02) complexed with calcium and barium ions and capped with ACE and NMA. I ran pdb2gmx, selecting the AMBER03 force field, and received an error r…

I have simulated a protein-ligand system using GROMACS 2020.6. Later, I extended the simulation and subjected it to production using GROMACS 2020.3. I didn’t encounter any error while executing the above steps. Will usage of different versions affect the accuracy of the trajectory? 1 post - 1 participant Read full topic

GROMACS version: 2020.6 GROMACS modification: Yes/No I am trying to minimize the energy of the system, during which I got some warnings related to the LINCS, specifically “relative constraint deviation after LINCS” (WARNING PASTED BELOW). I have some queries about the LINCS WARNING What is the meaning of this LINCS WARNING (below mentioned) If ignore the LINCS WARNING, how…

How to split membrane into 30*30 grid to calculate membrane curvature and and membrane surface 1 post - 1 participant Read full topic