The file formats are different for both,when I view them at ATB site (Automated Topology Builder site). My GROMACS version shows up only GROMOS96 53A6FF force-field.
Is there any difference between the two? I find the GROMACS version more easy to use.
Dear Apramita Chand:
One of important of those differences which you mentioned in your question is because of various force fildes.
Generally, there are three types of force fields:(1)all atom which the parameters provided for every single atom within the system.(2)united atom which the parameters provided for all atoms except non-polar hydrogens and (3) coarse grained which is an abstract representation of molecules by grouping several atoms into "super-atoms".
The force fields in GROMACS can be supported via;
AMBER
CHARMM
Coarse Grained Force Fields
GROMOS
OPLS
As of GROMACS version 4.5, the following seven AMBER force fields are natively supported:
AMBER94
AMBER96
AMBER99
AMBER99SB
AMBER99SB-ILDN
AMBER03
AMBERGS
Older GROMACS versions need a separate installation of the ffamber ports:Using AMBER Force Field in GROMACS - known as the "ffamber ports," a number of AMBER force fields, complete with documentation.
AMBER Force Fields - background about the AMBER force fields
AMBER Programs - information about the AMBER suite of programs for molecular simulation ANTECHAMBER/GAFF - Generalized Amber Force Field (GAFF) which is supposed to provide parameters suitable for small molecules that are compatible with the AMBER protein/nucleic acid force fields. It is available either together with AMBER, or through the antechamber package, which is also distributed separately. There is a script available for converting AMBER systems (set up, for example, with GAFF) to GROMACS (amb2gmx.pl), but it requires an AMBER installation to work.
The CHARMM27 force field has been ported to GROMACS and is officially supported as of version 4.5. For using CHARMM36 in GROMACS 5.0, please use the following settings in the .mdp file:
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no
GROMOS is is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be applied to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules.
GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 43b1, 45a3, 53a5 and 53a6. The GROMOS force fields are united atom force fields, i.e. without explicit aliphatic (non-polar) hydrogens.
GROMOS 53a6 - in GROMACS format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
GROMOS 53a5 - in GROMACS format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
GROMOS 43a1p - 43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine), and PTR (phosphotyrosine) (all PO42- forms), and SEPH, TPOH, PTRH (PO4H- forms).
OPLS (Optimized Potential for Liquid Simulations) is a set of force fields developed by Prof. William L. Jorgensen. There is both united atom (OPLS-UA) and all atom (OPLS-AA) forcefields.
I suggest you for using the last version of GROMACS for supporting a wide range of force- filled
Dear Apramita Chand:
Don't hesitate to contact me for any further discussion
Yes Sir .Thanks a lot for your reply. In gromacs itself, the gromos forcefields are present so I have to choose the gromacs 53a6 gromos version for downloading topology files rather than the ones adapted just for the gromos standalone versions.
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