Hi,
For 3. you can use the 'vector' action with the 'box' keyword to write
the box lengths, the 'vector' action with 'ucellx', 'ucelly', and/or
'ucellz' keyword(s) to get the X/Y/Z unit cell vectors, and the
'volume' action to calculate the total unit cell volume. See the
manual for full details.
-Dan
On Mon, Dec 14, 2020 at 4:06 PM Carlos <carlos.rom.74he.gmail.com> wrote:
>
> Hi dear all.
> I am trying to analyze what happens when we put certain acid near a
> membrane.
> I did the simulation from tutorial 14 from ambermd.org with the same files
> and the same input files and everything worked fine, but when I did
> every step by myself, it did not work very well, the hydrophilic heads of
> the lipids came out dispersed among the water molecules. I used the same
> input files but I make my sistem directly from charmm-gui.org.
>
> I noted that the box dimension changed. in tutorial 14 are:
> {81.355 80.001 70.549}, the same of DOPC_128.inpcrd file.
> but when I calculated this box in VMD these values were a little different:
> {86.665 85.300 76.234}
> In VMD I load prmtop and inpcrd files, and in the console I typed:
>
> set all [atomselect top all]
> measure center $all
> measure minmax $all
>
> My questions are:
> 1. why are they different if I put the same parameters suggested in
> tutorial 14
> 2. if the change of this water box could be causing the simulation to
> behave in this way.
> 3. how could I calculate well this water box.
>
> thanks in advance for your support
>
> Regards
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Received on Thu Dec 17 2020 - 09:30:03 PST
