[gmx-users] printing a trajectory file in readable format starting from a specific frame other than zero
Hello, Is there a function that allows users to read a trajectory file and print it in a readable format (like gmxdump) but starting from a user- specified frame rather than from 0? Thanks in advance, Silvia Crivelli -- 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! 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/Support/Mailing_Lists
[gmx-users] Fwd: gmx-users Digest, Vol 79, Issue 102
We have a visualization tool that allows us to visualize the changes in the energy during energy minimization. The areas with more intense color are those where the atoms contribute the most to the total energy value. I just wrote a plug-in to use Gromacs for energy minimizations (or MD simulations) and I need the per-atom energies to use our tool's energy visualization feature. Thanks again, Silvia Message: 3 Date: Sun, 14 Nov 2010 06:31:56 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to calculate per-atom energies To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cdee7ac.9020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 14/11/2010 5:58 AM, Silvia Crivelli wrote: Hello, When I run energy minimization, I'd like to obtain the energy per atom in addition to the (potential) energy value for the entire protein. Is there a way to do this? You can get the nonbonded energy per energy group, which you could define to be a single atom, but you are limited to 256 of such groups, and to not using PME. Otherwise, there are approaches involving a lot of hacking about with .top or .tpr files and using mdrun -rerun that could do this for both nonbonded and bonded. However, a more important issue before doing such work is to be sure about what you expect such a decomposition to tell you. A high or low energy for a given atom doesn't necessarily mean anything, and even if it did, the force field wasn't necessarily parametrized to produce reliable per-atom energies (though it probably does do so). Mark -- -- 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! 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/Support/Mailing_Lists
[gmx-users] how to calculate per-atom energies
Hello, When I run energy minimization, I'd like to obtain the energy per atom in addition to the (potential) energy value for the entire protein. Is there a way to do this? Thanks in advance, Silvia Crivelli -- 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! 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/Support/Mailing_Lists
[gmx-users] Question about building and testing on imac
Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make make install However, most of the tests (./gmxtest.pl simple and ./gmxtest.pl complex) FAILED. Could this be explained by the fact I'm using gcc4.2? If so, how can I compile with gcc4.0? If not, what could be the problem? I've tried this a couple of times (using single and double precisions) and got the same FAILED messages in all cases. Thanks in advance, Silvia -- 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! 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/Support/Mailing_Lists
[gmx-users] force evaluation
Hello, I need to calculate the forces (derivatives) for every atom in a protein as this is being locally minimized using mdrun. When I run mdrun I can get the maximum force F-max and the atom on which this force is evaluated printed in the log file (for example, F-max = 2.20323e+03 on atom 2641 .) I need to be able to compute the force value on every atom of the protein. How can I do this with Gromacs? I set the parameter nstfout = 10 in my .mdp file but this doesn't seem to make a difference. I'll really appreciate your help. Silvia ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
