On Mon, Nov 14, 2016 at 7:27 PM, Justin Lemkul <[email protected]> wrote:
> > > On 11/14/16 9:04 PM, Mohsen Ramezanpour wrote: > >> Thanks Justin for your comments. >> >> Comments interspersed. >> >> On Mon, Nov 14, 2016 at 6:47 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 11/14/16 5:11 PM, Mohsen Ramezanpour wrote: >>> >>> Dear Gromacs users, >>>> >>>> I have made an initial system with a number of molecules in a "large" >>>> box. >>>> >>>> Large means a box of size 50 50 50 nm? >>>> >>>> I am interested in the self-assembly process of molecules (parametrized >>>> in >>>> charmm36 ff) in the box. >>>> >>>> I expected pressure coupling to shrink the box quickly, but it seems it >>>> fails to do so. The simulation box did not change (ca. 0.5 nm in each >>>> direction) which seems strange to me. >>>> >>>> I have used four different P-couple schemes for 4 different type of >>>> self-assemblies: >>>> >>>> 1) isotropic >>>> >>>> pcoupl = berendsen >>>> pcoupltype = isotropic >>>> tau_p = 5.0 >>>> compressibility = 4.5e-5 >>>> ref_p = 1.0 >>>> >>>> >>>> 2) semiisotropic >>>> >>>> pcoupl = berendsen >>>> pcoupltype = semiisotropic >>>> tau_p = 5.0 >>>> compressibility = 4.5e-5 4.5e-5 >>>> ref_p = 1.0 1.0 >>>> >>>> >>>> 3) anisotropic with *fix shape* of box (*but the size could change*) >>>> >>>> pcoupl = berendsen >>>> pcoupltype = anisotropic >>>> tau_p = 5.0 >>>> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 >>>> ref_p = 1.0 1.0 1.0 0 0 >>>> 0 >>>> >>>> 4) anisotropic with *both size and shape able to change* >>>> >>>> >>>> pcoupl = berendsen >>>> pcoupltype = anisotropic >>>> tau_p = 5.0 >>>> compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 >>>> ref_p = 1.0 1.0 1.0 0 0 0 >>>> >>>> >>>> Here are some other parameters in mdp file which might be useful for >>>> finding the problem: >>>> >>>> integrator = md >>>> dt = 0.002 >>>> nsteps = 50000 >>>> nstlog = 1000 >>>> nstxout = 1000 >>>> nstvout = 1000 >>>> nstfout = 1000 >>>> nstcalcenergy = 100 >>>> nstenergy = 1000 >>>> >>>> cutoff-scheme = Verlet >>>> nstlist = 20 >>>> rlist = 1.2 >>>> coulombtype = pme >>>> rcoulomb = 1.2 >>>> vdwtype = Cut-off >>>> vdw-modifier = Force-switch >>>> rvdw_switch = 1.0 >>>> rvdw = 1.2 >>>> >>>> tcoupl = berendsen >>>> tc_grps = Molecules water_ions >>>> tau_t = 1.0 1.0 >>>> ref_t = 355 355 >>>> >>>> constraints = h-bonds >>>> constraint_algorithm = LINCS >>>> continuation = yes >>>> >>>> nstcomm = 100 >>>> comm_mode = linear >>>> comm_grps = Molecules WI >>>> >>>> >>>> You shouldn't reset COM motion like this. >>> >> >> >> Do you mean deviding it to Molecules and WI? If yes, could you please let >> me know why it is not approperiate? >> How if I use "system" instead? >> >> > Use System. Only layered systems should be considered for separate > comm_grps. Your approach risks the different groups having spurious > contributions from COM motion removal causing them collide. I've seen > crashes from it before. Sure. I will. I used this because I expected these lipids to eventually form a bilayer or HII phase. > > > >>> >>> refcoord_scaling = com >>> >>>> >>>> gen-vel = no >>>> >>>> I can make the initial system smaller, but I think starting from a large >>>> box would be better because it gives all the molecule enough freedom to >>>> move and assemble in better way. >>>> >>>> Is not it right to expect the p-couple shrink the box in nanoseconds? >>>> This >>>> was only for 100 ps but I expected more shrinkage of box. What do you >>>> think? >>>> >>>> >>>> 100 ps is nothing. >>> >>> >> Even if the box is not full with waters and there are a lot of empty >> spaces >> between molecules? >> >> > "A lot" is subjective, but in general, I stand by the statement that 100 > ps is nothing in this context. Agreed. Sorry for that. I think the example of 10*10*10 nm makes it clear now. The system had about 200 lipids and 50 waters/lipids. > > > >>> If you have a box full of water, as your settings above imply, >>> >> >> That is not the case, I have molecules and water, but there are plenty of >> empty spaces. >> >> > What is the purpose of void space? You're potentially introducing a lot > of artificiality. Perhaps you need to better explain your goals. Using > such a huge box is computationally very expensive, for potentially little > or no gain, plus the headaches associated with bizarre behavior due to > voids (which can also cause crashes). Your right. Based on the number of lipids (200 is reasonable) an water molecules I did not expect it to take too much time to fill these voids. I will make it smaller. > > >> you can't expect much of a change. Why do you need the box to shrink, or >>> why do you expect it to? >>> >> >> >> Based on the number of lipid molecules and waters I added to the box, and >> since the same system (with the same number of molecules and waters) will >> be in lamellat or other phases (in equilibrium) of smaller sizes (e.g. 10 >> 10 10 nm). i.e. if I make a bilayer out of these, it will be ca. >> 10*10*10 >> nm^3 in size >> >> >> A box will only shrink a lot if there is substantial void space, e.g. >>> intentional or due to a poor initial approximation of the system that >>> requires equilibration. >>> >>> Agreed. Regarding what I described about the system, do you think this is >> because 100 ps is not enough? Even for a small shrink of ~ 2 nm? >> >> > Impossible to predict. But again, 100 ps is not nearly enough time to > assess anything like what you're after. Sure, I will run longer But for smaller box as you suggested. Thanks for your comments Justin. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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