2015-10-19 15:16 GMT+02:00 David A Case <dacase.scarletmail.rutgers.edu>:
> 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.
>
> Now I see that there is also something funny with the density. It keep
increasing from 1.03 up to 1.053 and then it decrease.
I'm starting a new run. I'm not using the old 10ns simulation files. I'm
using pmemd.CUDA.
Well, when I use this script:
reference protein_complex.inpcrd
trajin prod1.traj.gz
trajin prod2.traj.gz
trajin prod3.traj.gz
trajin prod4.traj.gz
trajin prod5.traj.gz
autoimage
center :1-286 mass origin
image origin center familiar
rms ToRef :1-286.CA,C,N= reference out rmsd.arg mass
atomicfluct out rmsf.arg :1-286 byres
trajout protein_f.binpos binpos
go
everything looks fine.
But when I get rid of autoimage, center and image commands, I see that my
water box is spinning over the center of the protein and the protein is
sticking out of the water box.
And - yes, that is something different from what I've seen during old
simulations. I haven't seen anything like this before.
To this new simulations I've added the iwrap command and change the water
model to TIP3P.
> >
> > 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.
>
wat.pdb is water added by 3D-RISM, sorry for not mentioning about that at
the beginning.
I'll try to prepare this system without the combine command and the see
what will happen.
>
> 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.
>
I think that this spinning octahedral could be something funny.
But probably this is not the main problem. The problem is, I think, that I
probably have free spaces between water from 3D-RISM and tleap waterbox.
I can see them, whet I make a pdb file from my .prmtop and .crd files from
each step of simulation. After minimization I've got this free spaces, but
during heating and equilibration everything looks OK to me. And when I try
to make a .pdb file from production coordinates file, I see that the
waterbox looks quite normal, except it have a hole on one side, and my
protein sticking out form another side of the box.
That's kinda weird.
I think, I should change something during minimization.
I've found this script from D. SIndhikara's tutorial:
% minimization of solvent orientation
&cntrl
ntmin = 1,
imin = 1,
maxcyc = 1000,
ncyc = 250,
ntb = 1,
igb = 0,
ntr=1,
restraint_wt=10.0,
restraintmask='(:WAT.O) & ((!:WAT) <:5)',
ibelly=1,
bellymask=':WAT',
/
but I have no idea, when should I use it.
So, right now the question is - what should I do with this 'two waters' to
stop them from getting away from protein and/or prevent the protein from
sticking out of the water box.
If have any idea, please help.
Best regards,
Karolina Markowska
PhD student
> ....dac
>
>
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Received on Wed Oct 21 2015 - 02:30:03 PDT
