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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Received on Tue Feb 15 2022 - 08:30:03 PST
