# [gmx-users] Re:Time evolution of lipidbilayer

minnale minnale_gnos at rediffmail.com
Mon Jun 9 15:36:12 CEST 2008

```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&nbsp; <BR>=0Aminnale wrote:<BR>=0A&gt;<BR>=0A&gt;&nbsp; <BR>=0A&gt;&g=
t; Hi all,<BR>=0A&gt;&gt;&nbsp; This may be a trivial question<BR>=0A&gt;&g=
t;&nbsp; &nbsp;  I want to calculate &quot;time evolution of area per lipid=
&quot;<BR>=0A&gt;&gt; The steps I have done are<BR>=0A&gt;&gt; 1. Extracted=
BoxX and BoxY values of 5ns_popc.edr by using g_energy <BR>=0A&gt;&gt; com=
mand.<BR>=0A&gt;&gt; 2. I have written code for calculating area per lipid =
in way that boxX <BR>=0A&gt;&gt; multiply with boxY divided by 64<BR>=0A&gt=
;&gt; 3. I have got the plot in this way<BR>=0A&gt;&gt;&nbsp; &nbsp;  **0 t=
o 1000ps ---- started the value 0.609678 nm^2/N ended with <BR>=0A&gt;&gt; =
0.642679(shows high peak)<BR>=0A&gt;&gt;&nbsp; &nbsp;  **then 1000 to 4000p=
s&nbsp; shows silght variation with 0.64 value( <BR>=0A&gt;&gt; nearly stra=
ight line)<BR>=0A&gt;&gt;&nbsp; &nbsp;  **at 4000ps the value increased to =
0.653465 ( high peak) from <BR>=0A&gt;&gt; there it reduced again to 0.6478=
56 <BR>=0A&gt;&gt;<BR>=0A&gt;&gt; I want to ask you that the way values are=
got correct? and suggest me <BR>=0A&gt;&gt; some articles regarding area p=
er lipid<BR>=0A&gt;&gt;<BR>=0A<BR>=0A&gt;Your calculations seem reasonable,=
and you could also concatenate your <BR>=0A&gt;trajectories to get one con=
tinuous plot to make things simpler.&nbsp; The <BR>=0A&gt;value seems about=
right for POPC, but it's been a while since I &gt;checked <BR>=0A&gt;the e=
xact number.<BR>=0A<BR>=0A&gt;As far as literature goes, a simple Google se=
arch will turn up lots of <BR>=0A&gt;useful results.&nbsp; And if you're us=
ing the lipid parameters from <BR>=0A&gt;Tieleman's site, his publication l=
ist is a good place to start.<BR>=0A<BR>=0A-&gt;Justin<BR>=0A<BR>=0A&gt; &g=
t;Thanks for your aprreciation.<BR>=0A&gt;=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=