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
> > >
> > >
> > > /
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 15 2022 - 09:30:02 PST
