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Small molecule in CG simulation
- Bryan
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10 years 1 month ago #3548
by Bryan
Small molecule in CG simulation was created by Bryan
I am trying to simulate small molecule bound with protein complex.
I understand CG is really not suitable for doing this but this small molecule is only used us a barrier locate at the opening of ion channel. I have tried to generate topology file of small molecule. MD simulation failed and the error message come out like this. Can anyone help?
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Martini system from protein.pdb'
100000 steps, 2000.0 ps.
step 3100, will finish Tue Feb 25 16:54:43 2014imb F 6%
A list of missing interactions:
Bond of 4004 missing 1
Angle of 24 missing 6
Molecule type 'LIG'
the first 10 missing interactions, except for exclusions:
Angle atoms 6 8 7 global 754 756 755
Angle atoms 7 8 9 global 755 756 757
Angle atoms 7 6 8 global 755 754 756
Bond atoms 8 7 global 756 755
Angle atoms 8 9 7 global 756 757 755
Angle atoms 8 7 6 global 756 755 754
Angle atoms 9 7 8 global 757 755 756
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 356
Fatal error:
7 of the 7644 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
I understand CG is really not suitable for doing this but this small molecule is only used us a barrier locate at the opening of ion channel. I have tried to generate topology file of small molecule. MD simulation failed and the error message come out like this. Can anyone help?
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Martini system from protein.pdb'
100000 steps, 2000.0 ps.
step 3100, will finish Tue Feb 25 16:54:43 2014imb F 6%
A list of missing interactions:
Bond of 4004 missing 1
Angle of 24 missing 6
Molecule type 'LIG'
the first 10 missing interactions, except for exclusions:
Angle atoms 6 8 7 global 754 756 755
Angle atoms 7 8 9 global 755 756 757
Angle atoms 7 6 8 global 755 754 756
Bond atoms 8 7 global 756 755
Angle atoms 8 9 7 global 756 757 755
Angle atoms 8 7 6 global 756 755 754
Angle atoms 9 7 8 global 757 755 756
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 356
Fatal error:
7 of the 7644 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
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- jaakko
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10 years 1 month ago #3553
by jaakko
Replied by jaakko on topic Small molecule in CG simulation
Hi Bryan,
have you simulated the small molecule you parameterized alone (in solution)? Is it stable with the same time step? I'd start there if you haven't made sure of that already. Also using -rdd 1.6 helps with Martini due to the longer distance between bonded beads in CG.
- Jaakko
have you simulated the small molecule you parameterized alone (in solution)? Is it stable with the same time step? I'd start there if you haven't made sure of that already. Also using -rdd 1.6 helps with Martini due to the longer distance between bonded beads in CG.
- Jaakko
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