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keisuke-yanagisawa
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exprorer_msmd
MSMD (mixed-solvent molecular dynamics) engine and analysis tools
MIT License
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Res rmsd
#36
Ell112a
opened
3 weeks ago
1
Enabling to use MPS (Multi-Process Service) for better calculation efficiency
#35
Ell112a
closed
1 month ago
2
separate two position constraints: main chain / side chain
#34
keisuke-yanagisawa
opened
2 months ago
1
Disulfide CYX check
#33
keisuke-yanagisawa
opened
4 months ago
0
exprorer_msmd should immediately end with status non-zero if error happens
#32
keisuke-yanagisawa
opened
4 months ago
1
Top and Gro input
#31
keisuke-yanagisawa
opened
4 months ago
0
Update gromacs
#30
keisuke-yanagisawa
closed
3 months ago
0
tiny update
#29
keisuke-yanagisawa
closed
9 months ago
0
Disulfide bond auto detection
#28
keisuke-yanagisawa
opened
10 months ago
0
testing mamba installation (to solve libarchive.so.13 problem)
#27
keisuke-yanagisawa
closed
1 year ago
0
Boolean value shold not Strings
#26
iwatobipen
closed
1 year ago
2
Refactoring
#25
keisuke-yanagisawa
closed
1 year ago
0
Multimer input
#24
keisuke-yanagisawa
opened
1 year ago
1
Get the same results in total with the same index
#23
keisuke-yanagisawa
closed
4 months ago
3
ProteinSurfaceProfile, ProbeSurfaceProfile
#22
keisuke-yanagisawa
opened
1 year ago
0
PMAP
#21
keisuke-yanagisawa
opened
1 year ago
1
SimulationStep, Minimization, Heating, Equilibration, Production
#20
keisuke-yanagisawa
opened
1 year ago
0
Sequence
#19
keisuke-yanagisawa
opened
1 year ago
0
MSMD
#18
keisuke-yanagisawa
opened
1 year ago
0
SystemPreparator
#17
keisuke-yanagisawa
opened
1 year ago
0
SettingFileParser
#16
keisuke-yanagisawa
opened
1 year ago
0
raise ValueError if input protein has alternative coordinates
#15
keisuke-yanagisawa
opened
1 year ago
0
Slurm
#14
keisuke-yanagisawa
closed
1 year ago
0
Is it possible to run the code with SLURM ?
#13
iwatobipen
closed
1 year ago
3
use of .g96 file format to approve =>100000 atoms
#12
keisuke-yanagisawa
closed
1 year ago
1
Enable 0 mol/l of probe
#11
keisuke-yanagisawa
closed
1 year ago
1
Automate tests
#10
keisuke-yanagisawa
closed
1 year ago
1
Huge memory consumption in probe_profile
#9
keisuke-yanagisawa
closed
2 years ago
2
Use of OpenMM
#8
keisuke-yanagisawa
opened
2 years ago
0
Use GromacsWrapper instead of mdrun.sh
#7
keisuke-yanagisawa
opened
2 years ago
0
put pseudo repulsion centers on each atoms
#6
keisuke-yanagisawa
opened
2 years ago
3
Implement convergence check system
#5
keisuke-yanagisawa
opened
2 years ago
0
Pseudo repulsion preventing aggregation should be added for each probe atom, not COG.
#4
keisuke-yanagisawa
closed
2 years ago
0
consideration of sigma-hole of halogen atoms
#3
keisuke-yanagisawa
opened
2 years ago
2
unintended absolute path /workspaces/exprorer_msmd/output/test/prep1/virtual_repulsion.top (addvirtatom2top.py)
#2
keisuke-yanagisawa
closed
2 years ago
0
Use of absolute path as well as relative path (protein.conf, probe.conf)
#1
keisuke-yanagisawa
closed
2 years ago
1