[gmx-users] question about g_density

[Justin Lemkul]

On 2/14/14, 6:55 AM, jhosamelly wrote:
> Hi! Follow up question on this.
>
> I'm getting the xvg file i want but the interval is .5.
>
> This is too big for me since I want to get the bilayer thickness.
>

Bilayer thickness from g_density is probably not very accurate.

> what additional options should I add to
>
> g_density -f confout.gro -n index.ndx -o martini.xvg
>
> to get a better xvg output file.
>

You can tune the thickness of each slice by setting how many slices there are 
with -sl.

-Justin

> BTW, I increased the box size along the Z to have some vacuum on the system.
>
> when I haven't done this I got.
>
>           0                0
>      0.131134           21.208
>      0.262267           42.416
>      0.393401           42.416
>      0.524534          169.664
>      0.655668          381.744
>      0.786802          360.536
>      0.917935           212.08
>       1.04907          190.872
>        1.1802           42.416
>       1.31134                0
>       1.44247                0
>        1.5736                0
>       1.70474                0
>       1.83587                0
>         1.967                0
>       2.09814                0
>       2.22927                0
>        2.3604                0
>       2.49154                0
>       2.62267                0
>       2.75381                0
>       2.88494                0
>       3.01607                0
>       3.14721                0
>       3.27834                0
>       3.40947                0
>       3.54061                0
>       3.67174                0
>       3.80287                0
>       3.93401                0
>       4.06514                0
>       4.19628                0
>       4.32741                0
>       4.45854                0
>       4.58968                0
>       4.72081                0
>       4.85194           63.624
>       4.98308          127.248
>       5.11421          296.912
>       5.24534           318.12
>       5.37648          339.328
>       5.50761           84.832
>       5.63874           21.208
>       5.76988                0
>       5.90101                0
>       6.03215                0
>       6.16328                0
>       6.29441                0
>       6.42555                0
>
> density for P*.
>
> then when I increased the box size along the z the density output for P*
> became
>
>
>             0                0
>           0.5                0
>             1                0
>           1.5                0
>             2                0
>           2.5                0
>             3                0
>           3.5                0
>             4                0
>           4.5                0
>             5                0
>           5.5                0
>             6                0
>           6.5                0
>             7                0
>           7.5                0
>             8                0
>           8.5                0
>             9          5.56217
>           9.5          150.178
>            10          228.049
>          10.5                0
>            11                0
>          11.5                0
>            12                0
>          12.5                0
>            13                0
>          13.5                0
>            14          139.054
>          14.5          189.114
>            15                0
>          15.5                0
>            16                0
>          16.5                0
>            17                0
>          17.5                0
>            18                0
>          18.5                0
>            19                0
>          19.5                0
>            20                0
>          20.5                0
>            21                0
>          21.5                0
>            22                0
>          22.5                0
>            23                0
>          23.5                0
>            24                0
>          24.5                0
>
> Thanks guys! :)
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/question-about-g-density-tp5014454p5014536.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================