Yes, I did.
I compared my input and this tutorial's input, I did not find any restraint
flags for the production run. Therefore I went ahead to run my 100ns
simulation.
But I noticed that there is "RES" in the Heat up steps, and one step to
Hold. Is the Hold step a necessary step before production runs?
and thank you, Elvis, for the input. Tutorial uses ntp=2, I will use ntp=3
to give a try, and at the same time, I will try the "RES" flags in the
heat.in and then "hold.in" step.
On Tue, Feb 15, 2022 at 9:23 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> have you looked at the lipid tutorial?
> http://ambermd.org/tutorials/advanced/tutorial16/index.php
>
> On Tue, Feb 15, 2022 at 11:38 AM King Wu <lodking407.gmail.com> wrote:
>
> > 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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> >
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Received on Tue Feb 15 2022 - 10:00:03 PST
