[gmx-users] Re: density vs time?
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 5 23:02:59 CET 2008
xianghong qi wrote:
> Yes, you are right. I didn't apply pressure coupling and my simulation
> is under NVT.
> I just want to get the density of water vs time . Thanks so much .
>
You need to apply NPT conditions to get density information.
-Justin
> -Xianghong Qi
>
> On Wed, Nov 5, 2008 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Justin A. Lemkul wrote:
>
>
>
> Justin A. Lemkul wrote:
>
>
>
> xianghong qi wrote:
>
> Thanks, Justin:
>
> I use 4.0. Mine is here:
> -------------------------------------------------------------------
> 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR)
> 4 Coul.-recip. 5 Potential 6 Kinetic-En.
> 7 Total-Energy 8 Temperature 9
> Pressure-(bar) 10 Vir-XX 11 Vir-XY
> 12 Vir-XZ 13 Vir-YX 14 Vir-YY
> 15 Vir-YZ 16 Vir-ZX 17 Vir-ZY
> 18 Vir-ZZ 19 Pres-XX-(bar) 20
> Pres-XY-(bar)
> 21 Pres-XZ-(bar) 22 Pres-YX-(bar) 23
> Pres-YY-(bar) 24 Pres-YZ-(bar)
> 25 Pres-ZX-(bar) 26 Pres-ZY-(bar) 27
> Pres-ZZ-(bar) 28 #Surf*SurfTen
> 29 Mu-X 30 Mu-Y 31 Mu-Z
> 32 T-System
>
>
> ...and I really should not hit "send" until I'm done thinking. Are
> you applying pressure coupling in your simulation? Under NVT
> conditions, parameters like Volume and Density are not written,
> since volume is constant and density doesn't mean much without
> constant pressure.
>
>
> -Justin
>
>
> -Xianghong Qi
>
> On Wed, Nov 5, 2008 at 4:20 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> xianghong qi wrote:
>
> Hello, all:
>
> I checked the mailing list. Looks like g_energy
> can calculate
> density vs time, but
> my g_energy doesn't have options like density,
> volume? I am
> wondering how I can
> get my density vs time graph? Any suggestion is
> appreciated.
> Thanks.
>
>
> Look more closely. Both versions of Gromacs that I
> am currently
> using (3.3.3 and 4.0) have options for Density,
> Volume, and Box
> vectors as output from g_energy.
>
> -Justin
>
>
> -Xianghong Qi
>
>
>
> -- Some people make the world more
> special just by being in it.
>
>
>
> ------------------------------------------------------------------------
>
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> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
> (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> Some people make the world more special just by being in it.
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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