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Collagen parameters
- gupta.rakesh2
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6 years 11 months ago #7237
by gupta.rakesh2
Collagen parameters was created by gupta.rakesh2
Hello Everyone
I am trying to simulate the collagen molecule in presence of some nanoparticle. The collagen parameters were taken from this paper. (DOI: 10.1021/ct100015v)
I used Martinize.py script (with -collagen flag) for generating the CG structure and .itp file from the atomistic .pdb file (PDB ID: 4Z1R). The Martinize script gave backbone dihedrals parameter as 90.70 and 100 for theta and K respectively, however, in paper (DOI: 10.1021/ct100015v) a value of -89.3 and 100 reported.
I changed the parameter accordingly and ran simulation in presence of nanoparticle. So far, I have only managed to run it in NVT up to ~100 ns before the system explodes and gromacs shows following errors either "atom moved too far apart" or "segmentation fault" . I am using the Martini22 forcefield with Gromacs 5 and with the latest .mdp options. I have tried reducing the time step to 10 fs and 15 fs but still the problem persist. Even, I have tried with -rdd but still no luck.
Can anyone help me in it.
I am trying to simulate the collagen molecule in presence of some nanoparticle. The collagen parameters were taken from this paper. (DOI: 10.1021/ct100015v)
I used Martinize.py script (with -collagen flag) for generating the CG structure and .itp file from the atomistic .pdb file (PDB ID: 4Z1R). The Martinize script gave backbone dihedrals parameter as 90.70 and 100 for theta and K respectively, however, in paper (DOI: 10.1021/ct100015v) a value of -89.3 and 100 reported.
I changed the parameter accordingly and ran simulation in presence of nanoparticle. So far, I have only managed to run it in NVT up to ~100 ns before the system explodes and gromacs shows following errors either "atom moved too far apart" or "segmentation fault" . I am using the Martini22 forcefield with Gromacs 5 and with the latest .mdp options. I have tried reducing the time step to 10 fs and 15 fs but still the problem persist. Even, I have tried with -rdd but still no luck.
Can anyone help me in it.
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