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