Re:Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
Dear Justin I thought by use of -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me? thanks Fatemeh Ramezani -- 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
Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
On 4/15/13 3:01 AM, fatemeh ramezani wrote: Dear Justin I thought by use of -pairs I can calculate energy between any 2 groups from index file. when I use g_energy, result is a .xvg file that shows energy of system but I need to calculate energy between specific groups. is there any way for me? That is not what -pairs does, per the help description. If you want the energy of different components of the system (i.e. residues), you need to set appropriate energygrps in the .mdp file such that short-range nonbonded terms are decomposed. If you did not do this in your simulation, create a new .tpr file with appropriate groups and re-calculate the energies using the original trajectory with mdrun -rerun. Doing so does not decompose long-range terms (i.e. PME). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
On 4/14/13 9:38 AM, fatemeh ramezani wrote: Dear all After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error: No distance restraints in topology How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ? Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called nonbonded interaction energies decomposed by energy group, but whether or not you can call this an actual binding energy is highly questionable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
the command that I used is : g_energy -f md300.edr -s fws_md300.tpr -o energy.xvg -pairs pairs.xvg Fatemeh Ramezani From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 14 April 2013, 21:15 Subject: Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology On 4/14/13 9:38 AM, fatemeh ramezani wrote: Dear all After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error: No distance restraints in topology How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ? Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called nonbonded interaction energies decomposed by energy group, but whether or not you can call this an actual binding energy is highly questionable. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
On 4/14/13 3:09 PM, fatemeh ramezani wrote: the command that I used is : g_energy-f md300.edr -s fws_md300.tpr-o energy.xvg-pairs pairs.xvg The -pairs option is not relevant for what you are trying to do. From g_energy -h: Additionally running time-averaged and instantaneous distances between selected pairs can be plotted with the -pairs option. This option is only to be used when employing distance restraints, hence g_energy fails when it finds none. You need neither -pairs nor -s. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
