Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?
I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Sunday, October 19, 2014 2:31 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Wednesday, October 15, 2014 7:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?
Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. When calculation start, I got following warming message: ** WARNING: Listed nonbonded interaction between particles 27 and 159 at distance 2.056 which is larger than the table limit 2.029 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Wednesday, October 15, 2014 7:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?
On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote: Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? How is it that you're attempting to calculate this quantity? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] How long run should be enough for Free Energy Calculation of a protein?
Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- 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.