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Gromacs Forum
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3:18 AM
User discussions - GROMACS forums: Densmap and xpm2ps commands
posted on September 10, 2021 by Mehdi.Ghasemi

GROMACS version: GROMACS modification: Yes/No Here post your question Hi, Currently, I used gmx-densamp to get the 2D density of my desired atoms. As all you know, two separate outcomes can be taken. First, output.dat, which includes data in the matrix form, and the second one is output.xpm. My problem is when I check the data of output.dat and compare it with the color bar of …

 
 
5 hours later…
Gromacs Forum
Gromacs Forum
8:17 AM
User discussions - GROMACS forums: When pulling a group of a simulation system, how does each atom feel the pulling force?
posted on September 10, 2021 by Natsulait

GROMACS version: GROMACS modification: No Suppose two groups A and B (e.g, a protein and a ligand). We want to pull one group to dissociate. Then steered MD (SMD) would be a good choice. SMD pulls the centre of mass of one group to dissociate it from the other group. Then I have a question: (1) Does each atom feel the pulling forces? (2) Do the pulling forces act only on the…

 
 
6 hours later…
user1271772
user1271772
1:49 PM
Hi @dwhswenson!
 
 
10 hours later…
Gromacs Forum
Gromacs Forum
11:49 PM
User discussions - GROMACS forums: Terminal capping topology: how rtp and *.tdb are combined?
posted on September 10, 2021 by narwhal

GROMACS version: 2021.2 GROMACS modification: Yes: from Homebrew on mac Hi all, I have a problem when dealing with n terminal capping and/or c terminal capping for protein. I am using the charmm force field downloaded from MacKerell Lab Here I have my pdb file with the capping added manually: ATOM 1 CAY ACE U 0 -16.453 -12.961 -24.554 1.00 0.00 U4 C ATOM …

 

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