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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