HITS-MCM gromacs-ramd issues

HITS-MCM / gromacs-ramd

Random Acceleration Molecular Dynamics in GROMACS

GNU Lesser General Public License v2.1

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issues

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Using tauRAMD for binding

#40 FarzinSohraby opened 2 weeks ago
3
Compilation mistake

#39 RomainLaunay opened 1 month ago
1
The reference atom for periodic boundary conditions will not be considered

#38 BerndDoser closed 4 months ago
1
The simulation is not terminated after the ligand has exited the binding site using MPI

#37 BerndDoser closed 4 months ago
0
Set tpx_tag

#36 mabraham closed 6 months ago
3
how to install RAMD

#35 bigsmartguy closed 7 months ago
0
"Unknown left-hand 'ramd-force' .... in parameter file"

#34 wenchangzhou-qtx closed 8 months ago
1
Installation Error

#33 erolic closed 3 months ago
8
Synchronized trajectory output

#30 BerndDoser closed 1 year ago
1
New option `ramd-connected-ligands`

#29 BerndDoser closed 1 year ago
1
Acclerating only a part of the ligand

#28 kellegra opened 1 year ago
1
how do i install ramd when compiling gromacs

#27 Byun-jinyoung closed 2 years ago
1
ramd MD trajectories look strange

#25 satvikkg closed 3 years ago
3
Update to GROMACS 2021 and 2022

#24 BerndDoser closed 1 year ago
0
A RAMD run is likely not to restart properly.

#23 physicshinzui closed 3 years ago
5
I am wondering whether parameter names in the README are inconsistent with those in your software?

#22 physicshinzui closed 3 years ago
1
Last value in pullx- and pullf-file is zero

#21 BerndDoser closed 3 years ago
0
Remove RAMD forces after ligand has left the binding site

#20 BerndDoser closed 3 years ago
0
Write number of steps for every exit event

#19 BerndDoser closed 3 years ago
0
Wrong ligand-receptor distance using PBC

#18 BerndDoser closed 3 years ago
0
Units for the ramd-inputs

#17 kellegra closed 3 years ago
4
Treatment of pbc reference atoms

#16 BerndDoser closed 3 years ago
0
Manage multiple binding sites

#15 BerndDoser closed 3 years ago
2
Use ForceProvider interface to apply RAMD forces

#14 BerndDoser closed 3 years ago
0
Gromacs2020.3-RAMD1.1 error: Aborted (core dumped)

#13 satvikkg closed 3 years ago
5
Use gromacs stop condition after max distance is reached

#12 BerndDoser closed 3 years ago
0
Pull direction will not be updated for MPI workers

#11 BerndDoser closed 3 years ago
0
Write receptor-ligand COM distance to ramd.xvg file

#10 BerndDoser closed 3 years ago
1
COM distances are zero in pullx-file

#9 BerndDoser closed 3 years ago
0
Add documentation of RAMD input

#8 BerndDoser closed 4 years ago
0
Add regression test for 1WDHI example

#7 BerndDoser closed 4 years ago
0
Define new pull external potential provider RAMD and register it for grompp and mdrun

#6 BerndDoser closed 5 years ago
0
Test to reproduce PULL code result with RAMD code

#5 BerndDoser closed 5 years ago
0
Reuse PULL code for RAMD

#4 BerndDoser closed 5 years ago
0
Convert index group to atom index list for RAMD protein and ligand

#3 BerndDoser closed 5 years ago
0
Create RAMD input variables and read them from file md.mdp

#2 BerndDoser closed 5 years ago
0
Insert ramd branch for modifying forces as for pull code

#1 BerndDoser closed 5 years ago
1