[gmx-users] Re:Time evolution of lipidbilayer

[minnale]

Thanks for your prompt reply, 
Yes I will do further analysis a)thickness of bilayer b) g_order of popc by using 5ns trjectory file.

Thank you 

On Mon, 09 Jun 2008 Justin A.Lemkul wrote :
>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>
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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>
>>--Next_1213018572---0-202.137.237.238-31592--
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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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