[gmx-users] Cannot rename checkpoint file
Dear all Gromacs users, I am running MD simulation using Gromacs in Cluster. In my 3.5ns, it goes smooth and after that when i view my md.log file, it shows that File input/output error:Cannot rename checkpoint file; maybe you are out of quota? Please let me know how to rectify the error... But the MD job is running... Thank you with regards, S. KANNAN, RESEARCH SCHOLAR MOLECULAR QUANTUM MECHANICS LAB DEPT. OF PHYSICS BHARATHIAR UNIVERSITY COIMBATORE-46 TAMIL NADU INDIA mobile: 09095811314 -- 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] Interaction energy graph
Dear Gromacs users, i run dynamics for 20 ns and plot the interaction energy which i attached with this.. is this plot correct? Please suggest something Thank you kannan s india -- 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] Interaction energy
Dear Gromacs users, i run dynamics for 20 ns and plot the interaction energy which i attached with this.. is this plot correct? Please suggest something Thank you kannan s -- 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] Interaction energy graph
Dear Justin, Thank you very much for your reply.. I answer the above question, 1. I am doing the protein-ligand interaction(electrostati+vanderWaals). I took the 140 amino acid as a sequence which contains binding site of the protein in Chain A of protein. 2. why i choose this sequence is, to know the binding interaction in deep. my objective is what are the amino acid residues are important for the interaction with ligand and if we dock the ligand far away from the important amino acid residues(which is essential for strong binding), how the interaction energy varies. 3. while docking ligand with important amino acid residue, i get the 'A-plot', where as if i dock the ligand far away from this particular amino acid residue, i get the 'B-plot'. I think, my conclusion is that, the decreasing interaction in the B-plot is due to the lack of the particular one important amino acid residue. so this particular residue and its region is has more contribution in the binding... I attached both the A-plot and B-plot sir... is my conclusion correct from the graph? Thank you justin kannan s On Sat, Mar 15, 2014 at 7:15 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015170...@n6.nabble.com wrote: On 3/15/14, 2:17 AM, Kannan S wrote: Dear Gromacs users, i run dynamics for 20 ns and plot the interaction energy which i attached with this.. Attachments aren't allowed on the list. Link to a file if you want to share it. is this plot correct? No one here can know this. We don't know what the interaction energy is, or why you measured it, so correct is up to you and your knowledge of what you are doing. If you need help understanding how to correctly obtain interaction energies between species in the system, you need to tell us: 1. What you are studying 2. What your objective is 3. What you have tried to do to accomplish #2 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015170i=0 | (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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5015170i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Interaction-energy-graph-tp5015160p5015170.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/Interaction-energy-graph-tp5015160p5015189.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Interaction energy graph
Dear Justin, sorry sir i forget to attahc the files, it is here attached. Thank you very much for your reply.. I answer the above question, 1. I am doing the protein-ligand interaction(electrostati+vanderWaals). I took the 140 amino acid as a sequence which contains binding site of the protein in Chain A of protein. 2. why i choose this sequence is, to know the binding interaction in deep. my objective is what are the amino acid residues are important for the interaction with ligand and if we dock the ligand far away from the important amino acid residues(which is essential for strong binding), how the interaction energy varies. 3. while docking ligand with important amino acid residue, i get the 'A-plot', where as if i dock the ligand far away from this particular amino acid residue, i get the 'B-plot'. I think, my conclusion is that, the decreasing interaction in the B-plot is due to the lack of the particular one important amino acid residue. so this particular residue and its region is has more contribution in the binding... I attached both the A-plot and B-plot sir... is my conclusion correct from the graph? Thank you justin On Sat, Mar 15, 2014 at 7:15 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5015170...@n6.nabble.com wrote: On 3/15/14, 2:17 AM, Kannan S wrote: Dear Gromacs users, i run dynamics for 20 ns and plot the interaction energy which i attached with this.. Attachments aren't allowed on the list. Link to a file if you want to share it. is this plot correct? No one here can know this. We don't know what the interaction energy is, or why you measured it, so correct is up to you and your knowledge of what you are doing. If you need help understanding how to correctly obtain interaction energies between species in the system, you need to tell us: 1. What you are studying 2. What your objective is 3. What you have tried to do to accomplish #2 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015170i=0 | (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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5015170i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Interaction-energy-graph-tp5015160p5015170.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml A-plot.jpg (24K) http://gromacs.5086.x6.nabble.com/attachment/5015190/0/A-plot.jpg B-plot.jpg (21K) http://gromacs.5086.x6.nabble.com/attachment/5015190/1/B-plot.jpg -- View this message in context: http://gromacs.5086.x6.nabble.com/Interaction-energy-graph-tp5015160p5015190.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MM-GB/SA analysis in Gromacs
Dear Andrea Spitaleri, I run protein-ligand complex for 20ns simulation in gromacs, i need to calculate the binding free energy calculation. I had a look at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 , and i want to calculate MM/PBSA binding free energy using the tool you mentioned... So I kindly request you sir, to provide the valuable help sir... My email id is: kannan.2...@gmail.com I am waiting for your reply. Many thanks in advance kannan s -- View this message in context: http://gromacs.5086.x6.nabble.com/MM-GB-SA-analysis-in-Gromacs-tp5003337p5015014.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] pbc
Is there any problem when we analyse the protein-ligand complex simulation withPBC problem without using -trjconv? Thank you kannan s -- 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] pbc
Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its trajectory is same as old one. How to overcome this problem? Please give some suggestion. or shall i analyse without trjconv -pbc with raw trajector? Thank you best regards, kannan s On Fri, Jan 31, 2014 at 5:03 PM, Tsjerk Wassenaar [via GROMACS] ml-node+s5086n501418...@n6.nabble.com wrote: Hi Kannan, Depends a bit. Some tools handle PBC properly, some don't. Cheers, Tsjerk On Fri, Jan 31, 2014 at 9:30 AM, Kannan S [hidden email]http://user/SendEmail.jtp?type=nodenode=5014189i=0 wrote: Is there any problem when we analyse the protein-ligand complex simulation withPBC problem without using -trjconv? Thank you kannan s -- 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5014189i=1. -- Tsjerk A. Wassenaar, Ph.D. -- 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5014189i=2. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014189.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014191.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] pbc
Thank you very much for your valuable suggestion Justin... best regards, kannan s I On Fri, Jan 31, 2014 at 6:31 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5014192...@n6.nabble.com wrote: On 1/31/14, 7:09 AM, kannan wrote: Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its trajectory is same as old one. How to overcome this problem? Please give some suggestion. or shall i analyse without trjconv -pbc with raw trajector? As Tsjerk said, some tools handle PBC well, some don't. If you're having a specific issue with a specific tool, then you will need to account for periodicity effects. If not, then there is no need to worry. With protein-ligand systems and other complexes, -pbc nojump is usually the best first step. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5014192i=0 | (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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5014192i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014192.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4385198code=a2FubmFuLjI5MTBAZ21haWwuY29tfDQzODUxOTh8NjA3OTM5OTMw . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/pbc-tp5014184p5014210.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
