[gmx-users] simple question about umbrella pulling
Folks -- Reading Section 7.3.21 COM pulling in the GROMACS 4.0 manual, I don't quite see how to specify a nonzero minimum distance for an umbrella potential. I see that pull = umbrella pullgroup0 = ... pullgroup1 = ... pull_k1 = ... ; sets the force constant but I don't see how to set r0, for an umbrella potential between group0 and group1 of k1(r-r0)^2. Surely this is possible? Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] x2top hangs
Folks -- I cannot manage to get x2top to work on even the simplest example. Here is ethane.pdb, a PDB file for ethane (built using Avogadro, with the CONECT records stripped out): COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.2.2b1 ATOM 1 C LIG 1 -3.466 -1.641 -0.001 1.00 0.00 C ATOM 2 C LIG 1 -1.954 -1.689 0.025 1.00 0.00 C ATOM 3 H LIG 1 -3.817 -0.605 0.026 1.00 0.00 H ATOM 4 H LIG 1 -3.882 -2.168 0.863 1.00 0.00 H ATOM 5 H LIG 1 -3.850 -2.112 -0.910 1.00 0.00 H ATOM 6 H LIG 1 -1.570 -1.218 0.934 1.00 0.00 H ATOM 7 H LIG 1 -1.538 -1.163 -0.839 1.00 0.00 H ATOM 8 H LIG 1 -1.603 -2.726 -0.002 1.00 0.00 H END I try to run the following command under GROMACS 4.0, x2top -f ethane.pdb -o ethane.top with the most recent version of the file ffoplsaa.n2t in its proper place (/usr/local/gromacs/share/gromacs/top/), and I get the following output: ... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat Entries in elements.dat: 218 Looking whether force field files exist Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.n2t There are 23 name to type translations Generating bonds from distances... atom 0 ... and then the program hangs. Can someone confirm that x2top actually works, and send a simple working example to me? Scott Milner William H. Joyce Professor The Pennsylvania State University Department of Chemical Engineering 120 Fenske Laboratory University Park, PA 16802 (814) 863-9355 smil...@engr.psu.edu ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trouble compiling gromacs-3.3.2 on OS X 10.5.1
I'm trying to load gromacs on a new MacBook Pro, running 10.5.1 with latest developer tools installed. I get an error the first time I run ./configure, as follows: configure: error: Upgrade to binutils = 2.12.1 (or disable assembly loops). whereupon configure fails. What do I do to fix this? (Where is binutils so that I can upgrade it? Or what option to configure disables assembly loops, and what performance hit do I take if I do that?) ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] trouble compiling gromacs-3.3.2 on OS X 10.5.1
I don't mean to be ungrateful, but your reply was not *quite* explicit enough to actually be any help whatsoever. -- Scott On Jan 28, 2008, at 8:30 PM, Mark Abraham wrote: Scott Milner wrote: I'm trying to load gromacs on a new MacBook Pro, running 10.5.1 with latest developer tools installed. I get an error the first time I run ./configure, as follows: configure: error: Upgrade to binutils = 2.12.1 (or disable assembly loops). whereupon configure fails. What do I do to fix this? (Where is binutils so that I can upgrade it? Google will help you here. Or what option to configure disables assembly loops, and what performance hit do I take if I do that?) A big one. Mark ___ gmx-users mailing listgmx-users@gromacs.org 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 ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] trouble compiling gromacs-3.3.2 on OS X 10.5.1
Yes, I found this before I submitted my query. Of course things under OS X tend to be located in different places than GNU assumes. I ran the GNU install of binutils, and it did not change the behavior, perhaps because whatever gets installed isn't going to the right place where OS X keeps it. -- Scott On Jan 28, 2008, at 8:31 PM, DAVID RINCON wrote: It could be work: http://ftp.gnu.org/gnu/binutils/ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.___ gmx-users mailing listgmx-users@gromacs.org 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 ___ gmx-users mailing listgmx-users@gromacs.org 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
