I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the said force field. So, how do I include an additional force field in GROMACS? Or, can I even use other force fields not included in the package?
Dear Viejay Ordillo
When you study literature about MD simulation you should consider the software for example COMPASS is a forcefield in Material Studio. GLYCAM06 is a force field in AMBER software.
Albeit some severs could convert force filed between different software.
you should consider that developing a force file is hard and time consuming for researchers
I suggest finding a forcefield that is included in GROMACS, I think the GROMOS force field is suitable for your work.
Hope it helps
Dear Azadeh,
I understand the concern. But quite interestingly, I just found literature using cellulose models described by the GLYCAM06 force field simulated in GROMACS. Now I'm wondering how they were able to do it since the materials and methods sections did not specify conversion of force field files.
(https://www.diva-portal.org/smash/get/diva2:811757/FULLTEXT01.pdf)
Yes, you are right, it is also wondering for me you could ask for details of simulation from the authors of the paper with an email
Another way is that you could repeat the simulation by another force field such as GROMOS and compare the results. In my view, the force field is the same in general parameters such as Lennard Jones potential and also the GROMOS force field is suitable for biomolecules
Hope it helps
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