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

James Starlight jmsstarlight at gmail.com
Sat Sep 22 09:24:45 CEST 2012


I've integrated berger's lipid to the 54A7 force field in accordance
to your tutorial and simple change in my topol.top string to

#include "gromos54a7_lipid.ff/forcefield.itp"

and my simulation has been started without any warnings or errors.

But I'm not sure about Cut-offs in MDP files which I've used from my
simulation with gromos53a6_lipid.ff/

rlist		= 1.2		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.2		; short-range electrostatic cutoff (in nm)
rvdw		= 1.2		; short-range van der Waals cutoff (in nm)

does this values would be correct in 54A7 ff as well ?

What addition parameters of that ff should I take into account during
simulation of my protein-lipid system ? ( I'm simulate in npt ensemble
with SD integrator withot t_coupl )


2012/9/21, Justin Lemkul <jalemkul at vt.edu>:
> On 9/21/12 2:33 PM, James Starlight wrote:
>> Dear Gromacs Users!
>> In some recent publications about protein dynamics investigation I've
>> found reference about new gromos force field (56A7) where some fix in
>> case of dihedral terms have been included.
>> During my simulation performed with the 56A6 ff I've noticed that in
>> some cases short alpha helices fragments were unfolded during 50-100ns
>> of simulation. In particular that was in cases of simulation of
>> membrane receptors. In some of that proteins I've observed unfolding
>> of the part of the alpha helices which were placed in the water layer
>> ( the rest of the alpha helices embedded in the membrane layer was
>> very stable during all simulation time ). So I wounder to know if that
>> events were the artifacts of the 56A6 force field or there are some
>> biological-significance of such dynamics seen in the water layer.
>> Is it possible to obtain new 56A7 ff and integrate it into Gromacs (
>> I'm using version 4.54). ?
> 54A7 force field files can be obtained from ATB:
> http://compbio.biosci.uq.edu.au/atb/
>> Will the systems (topologies) made for 56A6 ff compatible with the
>> 56A7 ff ( In particular I'm using Berger's lipids) or should I create
>> my protein-in-membrane system again ?
> If you're using a different force field, you have to recreate the
> topologies.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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