Dear all greeting I am a new user in gromacs . To begin, I need to know how to generate date for simple water molecule and observe vibrational modes. I use this command as well as read in the manual: pdb2gmx -f prot.pdb -o prot.gro -p prot.top but when I choose
ff 43a1 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading prot.pdb... I have this error: Program pdb2gmx, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: prot.pdb On Fri, Apr 4, 2008 at 12:00 PM, <[EMAIL PROTECTED]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubI ascribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. RE: difference between pbc = full and pbc =xy (Berk Hess) > 2. Re: genion problem: is replacing 84 water molecules instead > of 200 (David van der Spoel) > 3. Re: Test-set problem with Gromacs 3.3.3 (David van der Spoel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 Apr 2008 03:50:40 +0200 > From: Berk Hess <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] difference between pbc = full and pbc =xy > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > All options are described in share/html/online/mdp_opt.html > pbc=xy is what you would (probably) guess pbc in x and y only. > pbc=full is replaced by periodic_molecules, such that it can also > be used with pbc=xy. > > Berk. > > > > From: [EMAIL PROTECTED] > > To: [email protected] > > Date: Thu, 3 Apr 2008 11:55:22 +0800 > > Subject: [gmx-users] difference between pbc = full and pbc =xy > > > > Dear all, > > > > I want to simulate an infinite inorganic surface in gmx 3.3.3 recently. As > I > > know, pbc = full is required for the bonded interaction on the edges. When > I > > check the newly CVS version, a new set named "pbc = xy" is implemented. I > > wonder if there is something different between the two sets. Thanks in > > advance. > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080404/99266df8/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 04 Apr 2008 08:08:44 +0200 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] genion problem: is replacing 84 water > molecules instead of 200 > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Subhrangshu Supakar wrote: > > Hi All !! > > I have defined my own system which contains 200 water molecules, which I > > can see in the .gro file. Then I created the .tpr file for 200 steps to > > steep. In the confout file I can again see the 200 water molecules. But > > When I am trying to replace the 200 water molecules with 200 Na+ > > GROMACS is complaining: > > genion -h is your friend. > > check the -rmin option. > > > > Replacing solvent molecule 144 (atom 4632) with Na > > Replacing solvent molecule 193 (atom 4779) with Na > > Replacing solvent molecule 49 (atom 4347) with Na > > Replacing solvent molecule 84 (atom 4452) with Na > > > > ------------------------------------------------------- > > Program genion, VERSION 3.3.2 > > Source code file: gmx_genion.c, line: 84 > > > > Fatal error: > > No more replaceable solvent! > > ------------------------------------------------------- > > It is replacing 84 water molecules only (I used genion for this) > > > > Can any body help me? > > > > Thanx in advance. > > > > Subhrangshu Supakar > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > ------------------------------ > > Message: 3 > Date: Fri, 04 Apr 2008 08:10:33 +0200 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Test-set problem with Gromacs 3.3.3 > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > [EMAIL PROTECTED] wrote: > > Dear gmx-users, > > > > I just updated my operating system to Centos 5.1 and Gromacs to version > > 3.3.3 and faced some problems with test-set (gmxtest-3.3.2.tgz). I can > > pass all the double precision tests (./gmxtest.pl -double all), but > > number of single precision tests are failed (./gmxtest.pl all). I looked > > at the files for these tests, and noticed that the corresponding tests > > include Coulombic and LJ 1-4 interactions, for which the calculated > > energies are all zero, whereas the reference energies are non-zero with > > values even 1000-2000 kJ/mol. Does anyone know reason for such differences? > > This actually points to possible compilation problems, and hence shows > the value of the test set. Please check every step in the compilation > process, and also which executable you are running (which mdrun) and > which libraries (ldd `which mdrun`). > > > > > > Thanks for your help, > > > > Janne > > > > > ------------------------------------------------------------------------------ > > > > Janne Hirvi, MSc(Physical Chemistry), Researcher > > University of Joensuu, Department of Chemistry, P.O.Box 111 80101 > > Joensuu, FI > > Tel: +358 13 2514544 & +358 50 3474223 > > E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use thewww > > interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 48, Issue 9 > **************************************** > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
