[gmx-users] RE: gmx-users Digest, Vol 105, Issue 5

First of all Happy New Year to everyone. Second, Justin I admire you. You keep this forum alive and very well tended. Great job.Third, Parisa, try running do_dssp with the flag -dt and pick an interval one or two orders of magnitude smaller than the length of your simulation. That should do it.

[gmx-users] RE: gmx-users Digest, Vol 104, Issue 114

Maria, You can place the export command in your .profile. That will get them to work. Use something like env | grep CPPFLAGS to make sure those settings are active before compiling gromacs. Best regards. Message: 6 Date: Thu, 27 Dec 2012 11:31:10 +0100 From: maria goranovic

Re: [gmx-users] conformational change

Morning Shine and Tsjerk, Sorry for the missing links (here and here), I was refering to PyMol wiki's and a blog: http://macosxpostdoc.blogspot.mx/2012/04/dssp-through-pymol.html http://www.pymolwiki.org/index.php/DSSP_Stride But what Tsjerk mentions is far more relevant, I was thinking

Re: [gmx-users] conformational change

Hello Shine, Besides what Justin mentioned you have to be careful of what you consider a helix or a loop. Pymol is note very accurate when it assigns secondary structure. I recommend you install dssp within Pymol (see here and here) and double check you secondary structure. Odds are that it

[gmx-users] .gro file format details

Good day, I was looking for the documentation for the .gro format but I couldn't find it on the site or manual. I am missing something?I am trying to parametrize some lipid ligands using ATB (http://compbio.biosci.uq.edu.au/atb) and I have been creating the .gro files by trial and error. I

[gmx-users] Re: .gro file format details

Thank you, Justin. I haven´t thought of that. Best regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!