On Fri, Dec 05, 2014, Sylvester Tumusiime wrote:
>
> You said the volume will decrease during equilibration based on the
> low density of the system. My question is how may i prevent this from
> happening? I suspect that once my volume decreases my solutes will leave
> or extend out of the box which i do not want.
You must have a density close to the experimental value, so you really don't
want to prevent the box from shrinking.
>
> Secondly, I used the add-ons command and it showed the ions forming
> a dense cloud outside the box which i suspect is a problem (will the
> minimization and equilibration steps bring them in?). That is why
> i wanted to specify the position of the ions. You suggest adding
> the ions to my PDB file in a position i like but i may have to add
> thousands. Will this call for a special script to do this?
If you have thousands of ions, LEaP may have problems (as I guess you have
seen.) I'd recommend using AddToBox to add the ions, or an external program
like packmol. There have been reports before like yours, where large numbers
of ions end up (apparently) outside the box.
>
> If i go ahead and add the ions to the position i want in the pdb file,
> am guessing i can use "TER" separator to place them between my solutes?
This is correct. The order of the ions (relative to solutes) is not
important.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 05 2014 - 06:00:10 PST
