My simulation system includes a protein and a membrane. I want to
investigate the dynamics of the protein with the presence of a membrane.
I used FF14SB for the protein and LIPID17 for the membrane. During the
equilibrium step, I first restrained the solute and simulated the water at
300K, then I heated up the whole system from low T to reach the RT without
restraint. Appropriate Na and Cl ions were added to neutralize the system.
The equ and production MD runs are in the explicit solvent model.
Please let me know if additional info is needed. I would be happy to
provide.
Thanks.
On Tue, Feb 15, 2022 at 8:26 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I think people might be able to offer help if you give a lot more
> information on exactly what you did, and what happened. For example, you
> don't say what force field you used for the lipid, or how you equilibrated
> it, or if water was included, and so on.
>
> On Tue, Feb 15, 2022 at 11:21 AM King Wu <lodking407.gmail.com> wrote:
>
> > Hi, Amber,
> >
> > I wonder if you received my previous email.
> >
> > I simulated a 100 ns simulation for a VMD generated POPC membrane. I
> > started with 120 X 80 A dimension, but got an aggregated/folded
> > conformation of the membrane after 100ns simulation. Do I miss any flags
> > of restrain in the input for my production run?
> > Because the screenshots are large in size, I could not attach them for
> your
> > reference.
> > Below is the input:
> >
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ioutfm = 1,
> > nstlim = 10000000,
> > dt = 0.002,
> > ntt = 3,
> > gamma_ln = 2.0,
> > ig = -1,
> > tempi = 300.0,
> > temp0 = 300.0,
> > ntp = 1,
> > ntb = 2,
> > ntc = 2,
> > ntf = 2,
> > cut = 12,
> > ntwr = 500,
> > ntpr = 500,
> > ntwx = 500,
> > ntwe = 500,
> > iwrap = 1,
> > ntr = 0,
> > /
> > $ewald
> >
> >
> > /
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Feb 15 2022 - 09:00:02 PST
