[gmx-users] Regarding density calculation
dallas.warren at monash.edu
Wed Oct 11 01:20:51 CEST 2017
1/ You should calculate the density of the system as a function of
time. Since the box will be expanding, contracting etc with time, you
should see if it has reached a dynamic equilibrium or not. This
normally settles down relatively quickly (see
https://twitter.com/dr_dbw/status/907735156382777344), but until you
look you don't know what is going on. You compare to experimental
values by looking it up (i.e. literature search and reference
textbooks) or actually physically measuring yourself the experimental
values for the same system.
2/ experimental density values are not calculated, they are measured.
You find the values in the literature and reference textbooks or
measure it yourself.
3/ first thing is look at the density as a function of time, as there
is a chance you have run for such a short time that the box has not
had time to contract to the correct size. Plus also ensure that, as
Mark mentioned, it is not a PBC artefact you are observing with the
visible voids (see
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On 10 October 2017 at 22:07, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> You can only compare to an experimental value by having available the
> results of an experiment... obviously you measure density by making a known
> composition and measuring its mass and volume.
> If you've equilibrated your volume in NPT, there are no voids. Anything you
> think is a void is being filled from the other side of the periodic box.
> On Tue, Oct 10, 2017 at 8:10 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>> I have ran a simulation of 1Gly+255 molecules of water, with my initial
>> box length being 2.10 nm, and after npt simulation, my final box length (in
>> the npt.gro file) is 2.090 nm.
>> For calculating the total density of the system, i used gmx energy command
>> gmx energy -f npt.edr -o density.xvg, and entered 22 followed by 0. I have
>> got the density of the system as 987.23 kg/m^-3.
>> 1] But my question is that how do i know this is the actual density of my
>> simulation system..?? how can i compare this with the experimental
>> 2] In Justin's lysozyme tutorials, in step seven, npt equilibration, it
>> states that the density of the system is 1006 kg/m^-3, which is close to
>> the experimental density value of 997.1 kg/m^-3 and the expected density of
>> tip3p model is 1002kg/m^-3.
>> How is the experimental density values calculated? where can the values be
>> 3] How do i know for my system that the density that i have got is correct.
>> (If i view the final npt.gro in vmd i can still see the voids/gaps/spaces
>> between the molecules, indicating that the box length must be still reduced
>> further.. or in other words, how can i compactly arrange the molecules in
>> my simulation box).
>> Any suggestions are highly appreciated....
>> With Best Regards,
>> Ph.D Student
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