GROMACS version: 2020.6 GROMACS modification: Yes/No Suppose there are two groups A and B. The centre of mass of each group is defined and the distance among them is denoted by d. Each group is pulled along the direction that is specified by pull-coord?-geometry = distance. By default, steered MD stops if d > L/2 where L is a side length of a periodic box. To avoid this, one …

GROMACS version: 2021.2 GROMACS modification: No I want to ask how to optimize GPU in gromacs, I use GPU 1660 Super, and have installed CUDA, I want to ask if GPU memory can in the upgrade, in the following picture I run gromacs but the GPU memory usage is only 679MB even though the 1660 Super memory is 6 GB, how do I upgrade the usage to 5-6 GB? SENT758×759 75.5 KB …

GROMACS version: gmx, version 2020.1-Ubuntu-2020.1-1 GROMACS modification: Yes/No Here post your question I have trying to generate my itp and top file using the pdb2gmx command. But as my structure does not have any parameters in the .rtp file of the forcefield I am getting an error. So I want to know how can I add a residue into the gromacs forcefield, so that I can generate …

GROMACS version: GROMACS modification: Yes/No Here post your question I need to run md simulation on my protein with an unnatural residue (formyl glycine). so I had to download charmm27.ff from SwissSidechain - A database of non-natural sidechains server to create the required topology. Then used 2 versions of GROMACS. the first one is gromacs-2016.4 applied to make topology, s…

GROMACS version: 2020.6 GROMACS modification: No Here post your question Hi Gromacs team, I am adding a new cap residue to the charmm36 forcefield. However, there is an H atom in the FOR residue (aldehyde group). ATOM 1608 C FOR B 111 -4.401 14.796 -50.833 1.00 0.00 ATOM 1609 O FOR B 111 -4.530 15.342 -51.930 1.00 0.00 ATOM 1610 H FOR B 111 …