On Thu, Oct 22, 2015 at 9:41 AM, Karolina Markowska <markowska.kar.gmail.com
> wrote:
> Thank you Jason for your reply.
>
> I'm running some test simulations right now, to find out, where is the
> problem.
>
> First of all - I've changed the prepration script from tleap, so I'm not
> using the combine command. I'm thinking that the combine command is sure
> messing something with my system. When I prepare the system without using
> the combine command, density and volume are equilibrating quicker.
>
> It looks like I don't quite understand, how does the iwrap work. I've
> looked into my .crd files and I've found out, that the water box isn't
> getting bigger at all.
> $ tail -1 protein_complex.inpcrd
> 74.2459799 74.2459799 74.2459799 109.4712190 109.4712190 109.4712190
> $ tail -1 emin3.rst (minimization)
> 74.2459799 74.2459799 74.2459799 109.4712190 109.4712190 109.4712190
> $ tail -1 emd1.crd (heating)
> 74.2459799 74.2459799 74.2459799 109.4712190 109.4712190 109.4712190
> $ tail -1 emd2.crd (equlibration)
> 71.2807594 71.2807594 71.2807594 109.4712190 109.4712190 109.4712190
> $ tail -1 prod1.crd (production)
> 71.3345282 71.3345282 71.3345282 109.4712190 109.4712190 109.4712190
> These values are the dimensions of my water box, am I right?
>
Yes.
>
> So it isn't getting any bigger during simulation.
The box is getting smaller, so the density is getting larger.
> But, as I can see in my prod1.out file, there is something like that:
>
> ...
> [snip]
>
> wrapping first mol.: -690.37099 33.66658 -524.81069
> ...
>
> Can you tell me, what is going on here?
>
It's wrapping a molecule from one side of the unit cell to the other
because the center of mass of that molecule has moved outside the
"designated" unit cell. This is what "iwrap" is doing, and it has no
effect on the simulation (just on the trajectory).
> Is it something related with the periodic boundaries?
> The volume is OK, the density is now OK, only the potential and total
> energy are decreasing.
>
So the system is relaxing. Do you have a specific reason for not
expecting that? Did you minimize? If not, then the dynamics, if it
doesn't blow up, will relax for you and the thermostat will pull the
"extra" energy out of the system. (By the way, ntt=1 is a poor choice for
thermostat -- ntt=3 is much better).
I thought that something is going on with the water box, because the
> density was growing, volume was decreasing, and total energy was decreasing
> too.
That by itself does not indicate a problem to me (in fact, I would say
even expected behavior). Why do you interpret this as a problem?
And after 50ns the system was barely moving. I thought before - that
> this is because there was no solvent so there were no interactions.
> Right now I don't have a clue, what is going on or how to fix it.
>
I don't know what "barely moving" means, so I can't comment on whether
this would be a problem or not. I'll let someone else address this if they
understand better than I do what you mean (and/or have seen this before).
I know the "flying block of ice" effect can make a solute appear to
"freeze", and this only happens with ntt=1 (one of many reasons why ntt=3
is a better choice), but I was under the impression that default settings
of nscm prevented this artifact.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 22 2015 - 07:30:05 PDT
