<P>
<BR>
Thanks for your prompt reply, <BR>
Yes I will do further analysis a)thickness of bilayer b) g_order of popc by using 5ns trjectory file.<BR>
<BR>
Thank you <BR>
<BR>
On Mon, 09 Jun 2008 Justin A.Lemkul wrote :<BR>
>trjcat, then do your analysis.<BR>
><BR>
>-Justin<BR>
><BR>
>minnale wrote:<BR>
>>Content-type: multipart/alternative;<BR>
>> boundary="Next_1213018572---0-202.137.237.238-31592"<BR>
>><BR>
>> This is a multipart mime message<BR>
>><BR>
>><BR>
>>--Next_1213018572---0-202.137.237.238-31592<BR>
>>Content-type: text/plain;<BR>
>> charset=iso-8859-1<BR>
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>><BR>
>>=0AThanks for your reply=0ACould you give me a clue about how can I make co=<BR>
>>ntinuous plot with concatenation of trajectories? if you tell any command t=<BR>
>>hat will be really helpful to me=0A=0AThanking you.=0A =0Aminnale wrote:=<BR>
>>=0A>=0A> =0A>> Hi all,=0A>> This may be a trivial question=0A>> I wan=<BR>
>>t to calculate "time evolution of area per lipid"=0A>> The steps I have don=<BR>
>>e are=0A>> 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_ene=<BR>
>>rgy =0A>> command.=0A>> 2. I have written code for calculating area per lip=<BR>
>>id in way that boxX =0A>> multiply with boxY divided by 64=0A>> 3. I have g=<BR>
>>ot the plot in this way=0A>> **0 to 1000ps ---- started the value 0.609=<BR>
>>678 nm^2/N ended with =0A>> 0.642679(shows high peak)=0A>> **then 1000 =<BR>
>>to 4000ps shows silght variation with 0.64 value( =0A>> nearly straight li=<BR>
>>ne)=0A>> **at 4000ps the value increased to 0.653465 ( high peak) from =<BR>
>>=0A>> there it reduced again to 0.647856 =0A>>=0A>> I want to ask you that =<BR>
>>the way values are got correct? and suggest me =0A>> some articles regardin=<BR>
>>g area per lipid=0A>>=0A=0A>Your calculations seem reasonable, and you coul=<BR>
>>d also concatenate your =0A>trajectories to get one continuous plot to make=<BR>
>> things simpler. The =0A>value seems about right for POPC, but it's been a=<BR>
>> while since I >checked =0A>the exact number.=0A=0A>As far as literature go=<BR>
>>es, a simple Google search will turn up lots of =0A>useful results. And if=<BR>
>> you're using the lipid parameters from =0A>Tieleman's site, his publicatio=<BR>
>>n list is a good place to start.=0A=0A->Justin=0A=0A> >Thanks for your aprr=<BR>
>>eciation.=0A><BR>
>>--Next_1213018572---0-202.137.237.238-31592<BR>
>>Content-type: text/html;<BR>
>> charset=iso-8859-1<BR>
>>Content-Transfer-Encoding: quoted-printable<BR>
>>Content-Disposition: inline<BR>
>><BR>
>><P>=0A<BR>=0AThanks for your reply<BR>=0ACould you give me a clue about how=<BR>
>> can I make continuous plot with concatenation of trajectories? if you tell=<BR>
>> any command that will be really helpful to me<BR>=0A<BR>=0AThanking you.<B=<BR>
>>R>=0A <BR>=0Aminnale wrote:<BR>=0A><BR>=0A> <BR>=0A>&g=<BR>
>>t; Hi all,<BR>=0A>> This may be a trivial question<BR>=0A>&g=<BR>
>>t; I want to calculate "time evolution of area per lipid=<BR>
>>"<BR>=0A>> The steps I have done are<BR>=0A>> 1. Extracted=<BR>
>> BoxX and BoxY values of 5ns_popc.edr by using g_energy <BR>=0A>> com=<BR>
>>mand.<BR>=0A>> 2. I have written code for calculating area per lipid =<BR>
>>in way that boxX <BR>=0A>> multiply with boxY divided by 64<BR>=0A>=<BR>
>>;> 3. I have got the plot in this way<BR>=0A>> **0 t=<BR>
>>o 1000ps ---- started the value 0.609678 nm^2/N ended with <BR>=0A>> =<BR>
>>0.642679(shows high peak)<BR>=0A>> **then 1000 to 4000p=<BR>
>>s shows silght variation with 0.64 value( <BR>=0A>> nearly stra=<BR>
>>ight line)<BR>=0A>> **at 4000ps the value increased to =<BR>
>>0.653465 ( high peak) from <BR>=0A>> there it reduced again to 0.6478=<BR>
>>56 <BR>=0A>><BR>=0A>> I want to ask you that the way values are=<BR>
>> got correct? and suggest me <BR>=0A>> some articles regarding area p=<BR>
>>er lipid<BR>=0A>><BR>=0A<BR>=0A>Your calculations seem reasonable,=<BR>
>> and you could also concatenate your <BR>=0A>trajectories to get one con=<BR>
>>tinuous plot to make things simpler. The <BR>=0A>value seems about=<BR>
>> right for POPC, but it's been a while since I >checked <BR>=0A>the e=<BR>
>>xact number.<BR>=0A<BR>=0A>As far as literature goes, a simple Google se=<BR>
>>arch will turn up lots of <BR>=0A>useful results. And if you're us=<BR>
>>ing the lipid parameters from <BR>=0A>Tieleman's site, his publication l=<BR>
>>ist is a good place to start.<BR>=0A<BR>=0A->Justin<BR>=0A<BR>=0A> &g=<BR>
>>t;Thanks for your aprreciation.<BR>=0A>=0A</P>=0A<br><br>=0A<Table borde=<BR>
>>r=3D0 Width=3D644 Height=3D57 cellspacing=3D0 cellpadding=3D0 style=3D'font=<BR>
>>-family:Verdana;font-size:11px;line-height:15px;'><TR><td><img src =3D'http=<BR>
>>://imadworks.rediff.com/cgi-bin/AdWorks/adimage.cgi/2129697_2122129/creativ=<BR>
>>e_2129852.gif' alt=3D'Amity' border=3D0></td></TR></Table><BR>
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>><BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
><BR>
</P>
<br><br>
<Table border=0 Width=644 Height=57 cellspacing=0 cellpadding=0 style='font-family:Verdana;font-size:11px;line-height:15px;'><TR><td><img src ='http://imadworks.rediff.com/cgi-bin/AdWorks/adimage.cgi/2129697_2122129/creative_2129852.gif' alt='Amity' border=0></td></TR></Table>