Moeed wrote:
Dear gmx users,
I tried to generate a stack of molecules using
*genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro*
I ran the MD simulation successfully but now I want to change the number
of molecules so that I get the desired system density. To do so I
played a bit with -dist and -box options but I find it not easy to reach
desired density. I need to have nearly 7 molecules per nm^3.
Regarding genbox program in the literature I see that it is recommended
for solvation of a solute in water. (The reason I want to try this is
because it seems I can directly enter the number of molecules with -nmol
option)
Where is this recommendation? The purpose of genbox is to add solvent. It is
up to the user to decide what that solvent is. For most simulations of
proteins, that solvent is indeed water, but you are by no means required to use
water.
You can add a specified number of molecules with -ci -nmol in tandem, not -nmol
alone.
1-I am sorry for asking ridiculous questions but does it make sense if I
use genbox and I ask the program solvate a single hexane molecule with
hexane molecules?
genbox –cp Hexane.gro –cs HExane.gro –p Hexane.top –o solvated.pdb
(although this command line is not working I want to know if there is
any way to modify the command to get it working or my idea is totally
wrong!)
You could do that, in theory. It's useless to say "it's not working" - no one
but you knows what that means. Probably your box size is insufficient.
2- Initialiy one single hexane molecule is in a box of 3*3*3 nm^3
(Hexane.gro). What is the best approach for doing such calculations. Can
I take any arbitrary box size and then based on the box size put a
specific No. of particles in it so that I get density?
You can specify whatever initial conditions you want. The true test of whether
your model is correct is whether or not that density is reproduced after
equilibration under some relevant thermodynamic ensemble. We can impose
whatever artificial starting configurations we want, but they are only useful if
they last through simulation.
Your original approach (using genconf) seems fine. Simulating that system
appropriately may converge to the density you want, within the inherent
limitations of the force field model chosen. Realize that you may never be able
to perfectly reproduce the experimentally-observed density. Even most water
models (that have been around for many years!) have not been able to do this.
-Justin
Thank you,
Hexane.gro:
**
Glycine aRginine prOline Methionine Alanine Cystine Serine
20
1HEX C1 1 1.786 1.639 1.501
1HEX H11 2 1.881 1.608 1.500
1HEX H12 3 1.768 1.696 1.421
1HEX H13 4 1.770 1.692 1.584
1HEX C2 5 1.693 1.518 1.499
1HEX H21 6 1.711 1.461 1.579
1HEX H22 7 1.710 1.465 1.416
1HEX C3 8 1.547 1.561 1.501
1HEX H31 9 1.528 1.617 1.420
1HEX H32 10 1.530 1.615 1.584
1HEX C4 11 1.454 1.440 1.500
1HEX H41 12 1.472 1.384 1.581
1HEX H42 13 1.472 1.386 1.418
1HEX C5 14 1.307 1.483 1.501
1HEX H51 15 1.289 1.539 1.420
1HEX H52 16 1.289 1.537 1.583
1HEX C6 17 1.214 1.361 1.500
1HEX H61 18 1.119 1.392 1.501
1HEX H62 19 1.231 1.307 1.418
1HEX H63 20 1.232 1.305 1.581
3.00000 3.00000 3.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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