Or the TNG format, supported in upcoming GROMACS 5.0, VMD sometime soon, and in its own API. TNG has state-of-the-art compression of coordinates *and* good single-file metadata.
Mark On Sun, Feb 23, 2014 at 1:35 PM, ABEL Stephane 175950 <stephane.a...@cea.fr>wrote: > Thanks Vitaly and Marks for you comments. > > I asked this question, because a collaborator is currently developing a > code that uses files in xyz format as input. As you said Mark, PDB/xyz are > not viable alternatives for analyzing data from large GROMACS (whatever > code) trajectories, so I have suggested to him to use others formats such > as xtc or dcd. > > > -------- > Stéphane Abel, PhD > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221 > Bat 528 Door 138C > Gif-sur-Yvette, F-91191 FRANCE > Phone (portable) : +33 6 49 37 70 60 > > ------------------------------ > > Message: 5 > Date: Sat, 22 Feb 2014 23:23:03 +0100 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org>, Vitaly > Chaban <vvcha...@gmail.com> > Subject: Re: [gmx-users] conversion xtc to xyz format with openbabel > Message-ID: > < > camnumasyzqff03cu-ollmm1wq5wnccnbyjjpdoti5bv_cub...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Sat, Feb 22, 2014 at 10:16 PM, Dr. Vitaly Chaban <vvcha...@gmail.com > >wrote: > > > The workaround is to "trjconv -o 111.pdb", open an editor, select a > > block of coordinates, and paste in XYZ file. > > > > I also do not like PDB files from gromacs, but AFAIK many programs > > generate such PDB files which other programs refuse to read. > > > > Yes, this is problematic. PDB was in active use before it had a spec, IIRC > :-) One problem implementing support for that in GROMACS is that you have > to *know* the element in order to write its symol, and this is very ugly to > support. Should we commit resources to writing and maintaining code to read > in databases to provide an imperfect mapping from reside and atom name to > element symbol for every supported force field? Or refuse to do editconf -f > in.gro -o out.pdb or trjconv -f in.trr -o out.pdb unless -s the.tpr is > supplied? Or accept that most tools probably cope with this particular > imperfection because there's lots of old tools that implement it? Or write > 'X' in those fields and deal with complaints from users of tools who see > that the field is present and do not use whatever heuristics they have for > coping with the empty field, or whose PDB-format trajectories are now twice > as large because every ATOM line has thirty extra spaces and an X? > > Mark > > > > > > Dr. Vitaly V. Chaban > > > > > > On Thu, Feb 20, 2014 at 12:47 PM, ABEL Stephane 175950 > > <stephane.a...@cea.fr> wrote: > > > Hello all, > > > > > > My apologies for these out topic questions > > > > > > Does anybody have already try to convert xtc trajectory into xyz with > > openbabel? > > > > > > Btw, it seems that pdb file generated with editconf can not be read by > > openbabel. I obtain the following error : > > > > > > WARNING: Problems reading a PDB file > > > Problems reading a HETATM or ATOM record. > > > According to the PDB specification, > > > columns 77-78 should contain the element symbol of an atom. > > > but OpenBabel found ' ' (atom 1) > > > > > > > > > Does anybody have a workaround? > > > > > > Thanks in advance > > > > > > > > > -------- > > > St?phane Abel, PhD > > > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221 > > > Bat 528 Door 138C > > > Gif-sur-Yvette, F-91191 FRANCE > > > Phone (portable) : +33 6 49 37 70 60 > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 6 > Date: Sat, 22 Feb 2014 21:08:17 -0300 > From: Marcelo Vanean <vanea...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Temperature coupling > Message-ID: > < > cad04euadgc8lwwatz_gwogc6uhu+7jpowco-8akd6z7wthn...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Michael Shirts, in this article is not discussed about the periodic > perturbation method to calculate viscosity. Anyway, thank you. > > On Sat, Feb 22, 2014 at 7:16 PM, Marcelo Vanean <vanea...@gmail.com> > wrote: > > Dr. Vitaly Chaban, I know that g_energy is doing all the work for me. > > However I want to understand the concepts. > > > > > > On Fri, Feb 21, 2014 at 6:38 PM, Marcelo Vanean <vanea...@gmail.com> > wrote: > >> > >> I am trying to calculate the viscosity of water (spc model) by periodic > >> perturbation method. The manual says (manual 4.6.5, pages 169 - 170): > "To > >> obtain the correct value for the viscosity the generated velocity > profile > >> should not be coupled to the heat bath, also the velocity profile > should be > >> excluded from the kinetic energy" and "The heat generated by the viscous > >> friction is removed by coupling to a heat bath". I don't understand. > How is > >> possible to couple the system to the thermal bath, but not the velocity > >> profile? > >> > >> Thank you in advance. > > > > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > End of gromacs.org_gmx-users Digest, Vol 118, Issue 94 > ****************************************************** > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.