GROMACS version: 2018.8 GROMACS modification: No I want to calculate the minimum distance of a group’s centroid to a protein, I don’t know how to definite the centorid of the group in the .ndx file. Would you like to tell me how to calculate the minimum distance of a group’s centorid to a protein? Thank you for your interest and response. Kind Regards Lili 1 post…

Hi all I am trying to use Gangle module for calculating angle between molecule and z axis. i guess gmx gangle can be used for that. The issue is molecule being symmetrical rotates around its principle axis as well. so i am having trouble defining atoms for vector. looking forward for suggestions from the group. I am not very clear about how plane selection works? can i use pla…

GROMACS version:2020.2 GROMACS modification:No Dear all gmx users, I want to conduct a simulation on a polymer, which is made up of numerous residues. I wrote the atom charges in the .rtp file, but most of these value have more than 6 decimal places (such as 0.123456789 ,etc.). It will give an error in the preparation of the .tpr file in the energy minimization which said …

GROMACS version: 2021.4 I’m working on a GROMACS plugin and we’re working on importing and viewing fep results in our software. Does anyone have an fep output file- non proprietary of course- that they’d be willing to share for test purposes? Thanks! 1 post - 1 participant Read full topic

GROMACS version: 2020.1-Ubuntu-2020.1-1 GROMACS modification: No Here post your question I can’t plot potential, PE or any analytical data in grace. It says "Can’t stat file potential.xvf ". Can anyone help me with this? 2 posts - 2 participants Read full topic