On Mon, Oct 19, 2015, Karolina Markowska wrote:
>
> I have a problem with my system. It's a small globular protein (286 aa).
> When I was doing short simulations (10 ns) there was no problem, but right
> now, when I want to do 50 ns simulations (5 x 10 ns) I see there is
> something wrong with the system.
> The volume is getting smaller, density is increasing and the total energy
> is decreasing very fast.
How much (numerically) is the density increasing? Are you starting the 50ns
simulations from the end of the 10ns run? Are you using sander or pmemd?
What do you see when you visualize the trajectory? Look *really* carefully to
see if there are any differences between the 10ns simulations and the 5x10ns
simulations.
>
> source leaprc.ff14SB
> loadAmberParams frcmod.ionsjc_tip3p
> solute = loadpdb protein.pdb
> solvent = loadpdb wat.pdb
> complex = combine {solute solvent}
I'm not sure what is in "wat.pdb". This command is just adding whatever water
might be there to the protein, the same as if you simply combined the protein
and water pdb files into a single PDB file.
I don't see anything wrong with your scripts. You could try setting iwrap=0:
there might be something funny with octahedral boxes. The fact that you have
some waters added through wat.pdb, and others added through solvateOct *might*
be causing a problem.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 19 2015 - 06:30:03 PDT
