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

[James Starlight]

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 ?

James

2012/9/22, James Starlight <jmsstarlight at gmail.com>:
> Justin,
>
>
> 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 )
>
> James
>
> 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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>