<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear Berk,<br>My system is quite complicated and extracting all bonds from individual molecule types will mean a lot of complicated logic in the script. Imho, the dump should list all bonds because it should show the processed topology. I can easily see the bonds per molecule type from the itp files, no need for a dump for this. Such change of the dump format is painful as you can see, because it breaks all scripts which were written for 3.x. Cracking the source is also not the best idea (what if I decide to run a script in a cluster overseas one day where it is not possible to recompile?)<br>May I put this as a feature request?<br>Meanwhile, is there any other way to list all bonds easily? If not, which source file should I modify?<br><br>Thanks in
advance,<br>Sincerely,<br><br>Semen<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Berk Hess <gmx3@hotmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, November 26, 2008 1:00:10 PM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] List of all bonds form tpr file?<br></font><br>
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I just realized that in 4.0 I modified things such that it only<br>prints the bonds per molecule type.<br>It would be quite easy to modify a program to write all bonds.<br>(mk_angdx for instance).<br><br>If you just have one atom type you can easily modify<br>your script by reading the number of molecules and atoms_mol<br>from the molblock print in the gmxdump output.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] List of all bonds form tpr file?<br>Date: Wed, 26 Nov 2008 11:52:45 +0100<br><br>
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Hi,<br><br>gmxdump in 4.0 still dumps all bonds.<br>I don't know what causes you not to see them.<br><br>Berk<br><br>> Date: Wed, 26 Nov 2008 02:09:08 -0800<br>> From: yesint4@yahoo.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] List of all bonds form tpr file?<br>> <br>> Dear All,<br>> We have a script, which visualizes the bonds in the coarse-grained system simulated in gromacs. In gromacs 3.x it was reading dumps of the tpr files and extracted BONDS records. Now in 4.x it does not work because gmxdump no longer outputs all bonds in the system. Is it possible to extract information about *all* bonds in the system (not only the bonds in each moleculetype) from tpr file in 4.x?<br>> <br>> Any help is appreciated!<br>> <br>> Semen<br>> <br>> <br>> <br>> <br>> ----- Original Message ----<br>> From: Mark Abraham <Mark.Abraham@anu.edu.au><br>> To: Discussion list for GROMACS users
<gmx-users@gromacs.org><br>> Sent: Wednesday, November 19, 2008 1:57:19 PM<br>> Subject: Re: [gmx-users] Pulling in 4.0 - Any documentation?<br>> <br>> Semen Esilevsky wrote:<br>> > Dear All,<br>> > Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file. Any help is appreciated!<br>> > <br>> > P.S. Probably the developers could put at least some very brief docs on web site while new manual is being prepared? Otherwise new cool features of 4.0 just can't be used by ordinary users...<br>> <br>> The beta manual is at <a target="_blank" href="ftp://ftp.gromacs.org/pub/beta/">ftp://ftp.gromacs.org/pub/beta/</a><br>> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list
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