[gmx-users] Gromos force fields and simulation of the alpha-helices membrane proteins

Justin Lemkul jalemkul at vt.edu
Sat Sep 22 14:11:41 CEST 2012

On 9/22/12 7:08 AM, James Starlight wrote:
> sorry I forgot to specify that I also refreshed topology for my
> protein by pdb2gmx.
> after I've created new 54a7_lipid.ff in the gromacs dir I applied
> pdb2gmx on the protein model only. Than I copied part of that new
> topology (with the parameters of protein) to old topology of the
> entirely system ( protein+lipids+water).  So I have protein and spc
> water parametrised in 54a7 ff and lipids - in berger's 53a6. If new
> 54a7 ff include only updates to dihedrals should I use old cut-offs ?

You will have to determine that yourself.  I use the 1.2 nm cutoffs for 
53A6+Berger because I found that they produce reasonable results.  I have no 
such insight for 54A7.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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