[gmx-users] genconf and density of system
Justin A. Lemkul
jalemkul at vt.edu
Thu May 13 23:07:31 CEST 2010
Moeed wrote:
> Hello,
>
> I intend to generate a stack of molecules with the command line:
>
> genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro
>
>
> Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7
> molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189
> molecuels. What I get from the above command is (-nbox 8 6 4 )192 but
Are you sure of that density? If so, your box dimensions give 27 nm^3, implying
that you'd have to put all 189 hexane molecules in that 3x3x3 box. Seems a bit
crowded to me, at least for a molecule of that size.
> the system size in getting bigger as well!. * 24.00000 18.00000
> 12.00000 nm^3.*
>
The only thing that genconf does is build replicates of a system, it does not
somehow intelligently pack your system together for you, so these dimensions are
exactly what you would expect: (8*3), (6*3), (4*3).
> Could you dear experts guide me how I can reach the system density I
> want. Also to I wanted to know what is best value -dist option. Is it ok
> if I leave the distance between boxes 0 0 0?
>
I've already told you a bit about the meaning (or lack thereof) in the density
of the initial configuration. You could conceivably simulate under a constant
volume ensemble once you have a suitable configuration, but then I'd argue that
you're forcing the density to be right and you're not using appropriate
conditions.
You can leave -dist set to zero, since the molecules are already in some sort of
box, and the -dist option just adds additional space between them, which is
probably not necessary.
The easiest method for building your system may simply be to decide on a box
size, determine the number of molecules that fit in it, and run:
genbox -ci hexane.gro -nmol (whatever) -box (whatever)
If all your molecules can be placed in the box, genbox will do it for you.
-Justin
> Thank you,
>
> Hexane-STACK.gro:
>
> Glycine aRginine prOline Methionine Alanine Cystine Serine
> 3840
> 1HEX C1 1 1.786 1.639 1.501 0.0000 0.0000 0.0000
> 1HEX H11 2 1.881 1.608 1.500 0.0000 0.0000 0.0000
> 1HEX H12 3 1.768 1.696 1.421 0.0000 0.0000 0.0000
> 1HEX H13 4 1.770 1.692 1.584 0.0000 0.0000 0.0000
> 1HEX C2 5 1.693 1.518 1.499 0.0000 0.0000 0.0000
> 1HEX H21 6 1.711 1.461 1.579 0.0000 0.0000 0.0000
> 1HEX H22 7 1.710 1.465 1.416 0.0000 0.0000 0.0000
> 1HEX C3 8 1.547 1.561 1.501 0.0000 0.0000 0.0000
> 1HEX H31 9 1.528 1.617 1.420 0.0000 0.0000 0.0000
> 1HEX H32 10 1.530 1.615 1.584 0.0000 0.0000 0.0000
> 1HEX C4 11 1.454 1.440 1.500 0.0000 0.0000 0.0000
> 1HEX H41 12 1.472 1.384 1.581 0.0000 0.0000 0.0000
> 1HEX H42 13 1.472 1.386 1.418 0.0000 0.0000 0.0000
> 1HEX C5 14 1.307 1.483 1.501 0.0000 0.0000 0.0000
> 1HEX H51 15 1.289 1.539 1.420 0.0000 0.0000 0.0000
> 1HEX H52 16 1.289 1.537 1.583 0.0000 0.0000 0.0000
> 1HEX C6 17 1.214 1.361 1.500 0.0000 0.0000 0.0000
> 1HEX H61 18 1.119 1.392 1.501 0.0000 0.0000 0.0000
> 1HEX H62 19 1.231 1.307 1.418 0.0000 0.0000 0.0000
> 1HEX H63 20 1.232 1.305 1.581 0.0000 0.0000 0.0000
> 2HEX C1 21 1.786 1.639 4.501 0.0000 0.0000 0.0000
> 2HEX H11 22 1.881 1.608 4.500 0.0000 0.0000 0.0000
> 2HEX H12 23 1.768 1.696 4.421 0.0000 0.0000 0.0000
> 2HEX H13 24 1.770 1.692 4.584 0.0000 0.0000 0.0000
> 2HEX C2 25 1.693 1.518 4.499 0.0000 0.0000 0.0000
> 2HEX H21 26 1.711 1.461 4.579 0.0000 0.0000 0.0000
> 2HEX H22 27 1.710 1.465 4.416 0.0000 0.0000 0.0000
> 2HEX C3 28 1.547 1.561 4.501 0.0000 0.0000 0.0000
> 2HEX H31 29 1.528 1.617 4.420 0.0000 0.0000 0.0000
> 2HEX H32 30 1.530 1.615 4.584 0.0000 0.0000 0.0000
> 2HEX C4 31 1.454 1.440 4.500 0.0000 0.0000 0.0000
> 2HEX H41 32 1.472 1.384 4.581 0.0000 0.0000 0.0000
> 2HEX H42 33 1.472 1.386 4.418 0.0000 0.0000 0.0000
> 2HEX C5 34 1.307 1.483 4.501 0.0000 0.0000 0.0000
> 2HEX H51 35 1.289 1.539 4.420 0.0000 0.0000 0.0000
> 2HEX H52 36 1.289 1.537 4.583 0.0000 0.0000 0.0000
> .
> .
> .
> .
> .
> 192HEX C1 3821 22.786 16.639 10.501 0.0000 0.0000 0.0000
> 192HEX H11 3822 22.881 16.608 10.500 0.0000 0.0000 0.0000
> 192HEX H12 3823 22.768 16.696 10.421 0.0000 0.0000 0.0000
> 192HEX H13 3824 22.770 16.692 10.584 0.0000 0.0000 0.0000
> 192HEX C2 3825 22.693 16.518 10.499 0.0000 0.0000 0.0000
> 192HEX H21 3826 22.711 16.461 10.579 0.0000 0.0000 0.0000
> 192HEX H22 3827 22.710 16.465 10.416 0.0000 0.0000 0.0000
> 192HEX C3 3828 22.547 16.561 10.501 0.0000 0.0000 0.0000
> 192HEX H31 3829 22.528 16.617 10.420 0.0000 0.0000 0.0000
> 192HEX H32 3830 22.530 16.615 10.584 0.0000 0.0000 0.0000
> 192HEX C4 3831 22.454 16.440 10.500 0.0000 0.0000 0.0000
> 192HEX H41 3832 22.472 16.384 10.581 0.0000 0.0000 0.0000
> 192HEX H42 3833 22.472 16.386 10.418 0.0000 0.0000 0.0000
> 192HEX C5 3834 22.307 16.483 10.501 0.0000 0.0000 0.0000
> 192HEX H51 3835 22.289 16.539 10.420 0.0000 0.0000 0.0000
> 192HEX H52 3836 22.289 16.537 10.583 0.0000 0.0000 0.0000
> 192HEX C6 3837 22.214 16.361 10.500 0.0000 0.0000 0.0000
> 192HEX H61 3838 22.119 16.392 10.501 0.0000 0.0000 0.0000
> 192HEX H62 3839 22.231 16.307 10.418 0.0000 0.0000 0.0000
> 192HEX H63 3840 22.232 16.305 10.581 0.0000 0.0000 0.0000
> * 24.00000 18.00000 12.00000*
>
>
>
> *******************Hexane.gro
> 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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