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HPMA polymer MARTINI parametrisation
- gmeleshko
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11 years 5 months ago #1281
by gmeleshko
HPMA polymer MARTINI parametrisation was created by gmeleshko
Dear all,
I am Ph.D student in Cardiff University, currently on my 3'rd year of research on polymer modelling. I have managed to collect some data on all-atomistic level and now are going to build a coarse-grained model using MARTINI ff.
The problem is I am working with synthetic polymer - HPMA (N-2-Hydroxypropyl methacrylamide) and I am going to adopt it to DL_POLY software in future(GROMAX is better option, but all my analysis tools are written in dl_poly and I think it should be possible to set up).
So could you please help me and suggest the best way of doing it. I can start from setting it up and running on GROMAX to have a benchmark, but I am not sure about parameters. As far as I can see I can try to divide by 3 beads - C2, P3 and P2. Can I then use parameters from available ff parameter sets to construct .itp file for GROMAX?
Also if there is anyone who had an experience of setting MARTINI on dl_poly, please let me know, so I can ask advice on couple of things.
I have just started working with MARTINI and now going through examples. But haven't really found out parametresation root for non-biological proteins, so please excuse me if my questions are a bit silly. Thanks for your attention.
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Regards,
Glib
I am Ph.D student in Cardiff University, currently on my 3'rd year of research on polymer modelling. I have managed to collect some data on all-atomistic level and now are going to build a coarse-grained model using MARTINI ff.
The problem is I am working with synthetic polymer - HPMA (N-2-Hydroxypropyl methacrylamide) and I am going to adopt it to DL_POLY software in future(GROMAX is better option, but all my analysis tools are written in dl_poly and I think it should be possible to set up).
So could you please help me and suggest the best way of doing it. I can start from setting it up and running on GROMAX to have a benchmark, but I am not sure about parameters. As far as I can see I can try to divide by 3 beads - C2, P3 and P2. Can I then use parameters from available ff parameter sets to construct .itp file for GROMAX?
Also if there is anyone who had an experience of setting MARTINI on dl_poly, please let me know, so I can ask advice on couple of things.
I have just started working with MARTINI and now going through examples. But haven't really found out parametresation root for non-biological proteins, so please excuse me if my questions are a bit silly. Thanks for your attention.
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Regards,
Glib
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