Dear Henry,<br><br>For Plot two .xgv files u can use following command<br><br><i>xmgrace file1.xvg file2.xvg</i><br><br>colour will come automatically in above case i think file1.xvg will be in BLACK and file2.xvg will be in RED (Its default), You can change aslo. <br>
U can add other .xvg file accordingly in above command to get plot for all the .xvg files in a single graph :) <br><br>Regards<br>Rituraj <br><br><div class="gmail_quote">On Tue, Dec 8, 2009 at 4:30 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. mpispawn.c:303 Unexpected exit status (shivkumar bale)<br>
2. gromacs.. (Henry Ynag)<br>
3. Re: Two Types of van de Waals interactions in one system<br>
(XAvier Periole)<br>
4. xmgrace plot (Henry Yang)<br>
5. Re: xmgrace plot (Jon Fuller)<br>
<br>
<br>
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<br>
Message: 1<br>
Date: Mon, 7 Dec 2009 23:15:44 -0600<br>
From: shivkumar bale <<a href="mailto:kumarbale@gmail.com">kumarbale@gmail.com</a>><br>
Subject: [gmx-users] mpispawn.c:303 Unexpected exit status<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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Message: 2<br>
Date: Tue, 8 Dec 2009 01:19:16 -0800 (PST)<br>
From: Henry Ynag <<a href="mailto:henryynag@yahoo.com">henryynag@yahoo.com</a>><br>
Subject: [gmx-users] gromacs..<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:903781.22164.qm@web113919.mail.gq1.yahoo.com">903781.22164.qm@web113919.mail.gq1.yahoo.com</a>><br>
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<br>
Hello everyone,<br>
<br>
I am quite new to gromacs. I would like to know how can I calculate the area per lipid for my simulations. I am running simulations with 128 DMPC lipid bilayer. I have the output of 30 ns simulations. Also how can i make a graph with this output.<br>
<br>
Any help!<br>
<br>
Henry<br>
Biochemistry<br>
<br>
<br>
<br>
<br>
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Message: 3<br>
Date: Tue, 8 Dec 2009 10:52:00 +0100<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] Two Types of van de Waals interactions in one<br>
system<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:7ECBCABE-B1AF-45E5-9723-1D87364FBF9B@rug.nl">7ECBCABE-B1AF-45E5-9723-1D87364FBF9B@rug.nl</a>><br>
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<br>
One solution would be to use tabulated potential for which the<br>
analytical form does not matter.<br>
<br>
On Dec 8, 2009, at 4:29 AM, Mark Abraham wrote:<br>
<br>
> hong bingbing wrote:<br>
>> Dear all,<br>
>> Has anyone tried to use 2 van de Waals interaction types in one<br>
>> system? For example, the system includes two components A and B.<br>
>> The van de Waas interaction for A is LJ type, while for B<br>
>> Buckingham form is used. Can GROMACS support two forms<br>
>> simultaneously?<br>
><br>
> No. How would you describe the vdW interaction between an atom from<br>
> A and one from B?<br>
><br>
> If the reason for this question is based on a desire to mix two<br>
> force fields - don't.<br>
><br>
> Mark<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 8 Dec 2009 02:51:12 -0800 (PST)<br>
From: Henry Yang <<a href="mailto:henryynag@yahoo.com">henryynag@yahoo.com</a>><br>
Subject: [gmx-users] xmgrace plot<br>
To: gromacs <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:975347.17369.qm@web113912.mail.gq1.yahoo.com">975347.17369.qm@web113912.mail.gq1.yahoo.com</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hello everyone,<br>
<br>
I am also new to xmgrace. I have two .xvg file which I have got from the simulation data analysis. How can I open both of them in one xmgrace graph with two distinct color? How can I proceed with the comand?<br>
<br>
I know this is very basic but I have to learn!<br>
Pls give me response.<br>
<br>
Henry<br>
Biochemistry<br>
<br>
<br>
<br>
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Message: 5<br>
Date: Tue, 8 Dec 2009 10:53:25 +0000<br>
From: Jon Fuller <<a href="mailto:jonathan.fuller@gmail.com">jonathan.fuller@gmail.com</a>><br>
Subject: Re: [gmx-users] xmgrace plot<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:76dd1c620912080253t6b8ce2dehfa65e42bda43a231@mail.gmail.com">76dd1c620912080253t6b8ce2dehfa65e42bda43a231@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
>From the command line you can type xmgrace file1.xvg file2.xvg (where file1<br>
and file2 are the filenames!).<br>
<br>
Jon<br>
<br>
2009/12/8 Henry Yang <<a href="mailto:henryynag@yahoo.com">henryynag@yahoo.com</a>><br>
<br>
> Hello everyone,<br>
><br>
> I am also new to xmgrace. I have two .xvg file which I have got from the<br>
> simulation data analysis. How can I open both of them in one xmgrace graph<br>
> with two distinct color? How can I proceed with the comand?<br>
><br>
> I know this is very basic but I have to learn!<br>
> Pls give me response.<br>
><br>
> Henry<br>
> Biochemistry<br>
><br>
><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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End of gmx-users Digest, Vol 68, Issue 44<br>
*****************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------------------------------<br>RITURAJ PUROHIT<br>Assistant Professor, Bioinformatics Division<br>
School of Bio-sciences and Technology (SBST)<br>Vellore Institute of Technology, University<br>Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.<br>Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)<br>Fax; +91-416-2243092, E-mail: <a href="mailto:rituraj@vit.ac.in">rituraj@vit.ac.in</a><br>
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