From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Mar 19 2012 - 07:42:46 CDT
On Sun, Mar 18, 2012 at 13:19, Albert <mailmd2011_at_gmail.com> wrote:
> I've built a membrane system in CHARMM GUI and I found that it generate
> seven .inp file for NAMD running:
Those input files are not for NAMD but for CHARMM!
> step6.1_equilibration.inp step6.3_equilibration.inp
> step6.5_equilibration.inp step7.1_production.inp
> step6.2_equilibration.inp step6.4_equilibration.inp
> I am wondering what each .inp does? could anybody give a brief comments on
> each .inp?
Open those files with a text editor and you will see what each of the
files does (I just mention two things: minimization, equilibration).
You need to buy CHARMM to make use of those files or just "transcribe"
them to NAMD.
> I also find that we can use NPT, NPAT and NPγT for ensemble. However, we
> have to assign surface tension for NPAT or NPγT. I am wondering how much
> should we use for NPAT or NPγT? and I am confused at the unit for those
> surface tension because it use xxx/cm?
You can only assign a artificial tension to NPgT simulations. The unit
is dyne/cm^2. You probably want to use NPAT or NPgT to adjust the
membrane to some real word experiments if you have some or can find
some in the literature for your exact membrane composition, otherwise
you are better of with NPT (of course I do not know what you want to
simulate and observe).
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