[gmx-users] Re:Time evolution of lipidbilayer
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 9 15:38:26 CEST 2008
trjcat, then do your analysis.
-Justin
minnale wrote:
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> =0AThanks for your reply=0ACould you give me a clue about how can I make co=
> ntinuous plot with concatenation of trajectories? if you tell any command t=
> hat will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:=
> =0A>=0A> =0A>> Hi all,=0A>> This may be a trivial question=0A>> I wan=
> t to calculate "time evolution of area per lipid"=0A>> The steps I have don=
> e are=0A>> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_ene=
> rgy =0A>> command.=0A>> 2. I have written code for calculating area per lip=
> id in way that boxX =0A>> multiply with boxY divided by 64=0A>> 3. I have g=
> ot the plot in this way=0A>> **0 to 1000ps ---- started the value 0.609=
> 678 nm^2/N ended with =0A>> 0.642679(shows high peak)=0A>> **then 1000 =
> to 4000ps shows silght variation with 0.64 value( =0A>> nearly straight li=
> ne)=0A>> **at 4000ps the value increased to 0.653465 ( high peak) from =
> =0A>> there it reduced again to 0.647856 =0A>>=0A>> I want to ask you that =
> the way values are got correct? and suggest me =0A>> some articles regardin=
> g area per lipid=0A>>=0A=0A>Your calculations seem reasonable, and you coul=
> d also concatenate your =0A>trajectories to get one continuous plot to make=
> things simpler. The =0A>value seems about right for POPC, but it's been a=
> while since I >checked =0A>the exact number.=0A=0A>As far as literature go=
> es, a simple Google search will turn up lots of =0A>useful results. And if=
> you're using the lipid parameters from =0A>Tieleman's site, his publicatio=
> n list is a good place to start.=0A=0A->Justin=0A=0A> >Thanks for your aprr=
> eciation.=0A>
> --Next_1213018572---0-202.137.237.238-31592
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> <P>=0A<BR>=0AThanks for your reply<BR>=0ACould you give me a clue about how=
> can I make continuous plot with concatenation of trajectories? if you tell=
> any command that will be really helpful to me<BR>=0A<BR>=0AThanking you.<B=
> R>=0A <BR>=0Aminnale wrote:<BR>=0A><BR>=0A> <BR>=0A>&g=
> t; Hi all,<BR>=0A>> This may be a trivial question<BR>=0A>&g=
> t; I want to calculate "time evolution of area per lipid=
> "<BR>=0A>> The steps I have done are<BR>=0A>> 1. Extracted=
> BoxX and BoxY values of 5ns_popc.edr by using g_energy <BR>=0A>> com=
> mand.<BR>=0A>> 2. I have written code for calculating area per lipid =
> in way that boxX <BR>=0A>> multiply with boxY divided by 64<BR>=0A>=
> ;> 3. I have got the plot in this way<BR>=0A>> **0 t=
> o 1000ps ---- started the value 0.609678 nm^2/N ended with <BR>=0A>> =
> 0.642679(shows high peak)<BR>=0A>> **then 1000 to 4000p=
> s shows silght variation with 0.64 value( <BR>=0A>> nearly stra=
> ight line)<BR>=0A>> **at 4000ps the value increased to =
> 0.653465 ( high peak) from <BR>=0A>> there it reduced again to 0.6478=
> 56 <BR>=0A>><BR>=0A>> I want to ask you that the way values are=
> got correct? and suggest me <BR>=0A>> some articles regarding area p=
> er lipid<BR>=0A>><BR>=0A<BR>=0A>Your calculations seem reasonable,=
> and you could also concatenate your <BR>=0A>trajectories to get one con=
> tinuous plot to make things simpler. The <BR>=0A>value seems about=
> right for POPC, but it's been a while since I >checked <BR>=0A>the e=
> xact number.<BR>=0A<BR>=0A>As far as literature goes, a simple Google se=
> arch will turn up lots of <BR>=0A>useful results. And if you're us=
> ing the lipid parameters from <BR>=0A>Tieleman's site, his publication l=
> ist is a good place to start.<BR>=0A<BR>=0A->Justin<BR>=0A<BR>=0A> &g=
> t;Thanks for your aprreciation.<BR>=0A>=0A</P>=0A<br><br>=0A<Table borde=
> r=3D0 Width=3D644 Height=3D57 cellspacing=3D0 cellpadding=3D0 style=3D'font=
> -family:Verdana;font-size:11px;line-height:15px;'><TR><td><img src =3D'http=
> ://imadworks.rediff.com/cgi-bin/AdWorks/adimage.cgi/2129697_2122129/creativ=
> e_2129852.gif' alt=3D'Amity' border=3D0></td></TR></Table>
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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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