[gmx-users] Forcefield to choose

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 5 15:04:53 CEST 2008

vivek sharma wrote:
> Hi everybody,
> I am running MDS for protein molecule using GROMACS, but I am not sure 
> of which forcefield I should use.
> Can anybody suggest me the criteria for choosing forcefield ?

Every force field has its inherent benefits and limitations.  There is no 
substitute for studying up on each (by reading the primary literature), and 
choosing the one best suited to your system.  A bit of a shortcut would be to 
look into the literature for similar systems and see what people are using.

> Also, I am using drug-enzyme tutorial by John E. Kerrigan titled 
> "GROMACS Tutorial for Drug – Enzyme Complex." where it is suggested to 
> use PRODRG server for residues whose entry is not available in .rtp. In 
> this tutorial it is suggested to edit the .gro and .top file manually, 
> Can anybody suggest any other way (may be some tool or command) of doing 
> such editing (not manually).

As in, separating the ligand and protein coordinates from each other?  I suppose 
trjconv could do it, but it really is a trivial task to use a text editor... 
IIRC, the tutorial walks you through every step of modifying the 
PRODRG-generated topology.

Also note that if you use PRODRG/PRODRG2.5 your force field has already been 
chosen for you (ffgmx in the case of PRODRG and ffG43a1 for PRODRG2.5).  If this 
is not suitable, then you have a difficult task of parameterization ahead!


> With Thanks
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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