[gmx-users] Regarding the forcefield, topology..

[petar.zuvela]

Hi Dilip,

There is no clear recipe for which force field to use. It depends on the particular system. First thing you should do is perform a literature search to check for similar systems and md conditions.

Next, you shouldn't mix force fields. Use the same FF for both macromolecules and small org molecules.

As for parameterizaiton of FF parameters for molecules you mentioned, both Amber and CHARMM FF have general force fields for them as well as tools to parameteize thwm (e.g., antechamber) . They also procide tools for their easy conversion into gromacs format.

Hope this helps.

Regards,
Petar





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-------- Original message --------
From: Dilip H N <cy16f01.dilip at nitk.edu.in>
Date: 6/12/17 11:29 AM (GMT+08:00)
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Regarding the forcefield, topology..

Hello,
1] I want to simulate molecules such as Methylamine(CH3NH2),
Dimethylamine((CH3)2NH), Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3
)3NO-).
Can anybody suggest me the right forcefield in gromacs for these
molecules....in which forcefield is this available along with its residues..
2] Are the forcefields for all these molecules available in the same
forcefield..?
3] and thn i want to simulate an aminoacid with the above molecules...how
can i simulate if the aminoacid and the above said molecules are in
different forcefields..??

Thank you

--
With Best Regards,

DILIP.H.N
Ph.D Student



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