Hello!
I looks like everything is OK now with my simulations. Once again thank you
for your help.
Could someone explain me something more about that "flying block of ice
effect"?
And I would appreciate if you also tell me some differences between the
Berendsen and Langevin thermostat. Maybe there is a paper about these two
thermostats?
Looking forward to your reply.
Have a nice day,
Karolina
2015-10-23 16:26 GMT+02:00 Karolina Markowska <markowska.kar.gmail.com>:
> Dear Jason,
>
> Thank you very very much!
> I think you solved my problem!
>
> You're right, the water box is getting smaller, I haven't noticed it
> before.
>
> I think I was observing the "flying block of ice" effect. My protein just
> freeze, as you can see from the RMSD plot (from heating, equilibration and
> 50ns production). It's on the same moment, when the water box gets smaller.
> https://www.dropbox.com/s/n4ki045pmoqfpmk/rmsd.png?dl=0
>
> I'll try to run a 50ns simulation using ntt=3 and see what will happen.
>
> Have a nice day!
>
> Karolina
>
>
> 2015-10-22 16:05 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
>
>> 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 Mon Oct 26 2015 - 06:00:05 PDT
