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: >>Content-type: multipart/alternative; >> boundary="Next_1213018572---0-202.137.237.238-31592" >> >> This is a multipart mime message >> >> >>--Next_1213018572---0-202.137.237.238-31592 >>Content-type: text/plain; >> charset=iso-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >>=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 >>Content-type: text/html; >> charset=iso-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >><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-- >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > >-- ======================================== > >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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