[gmx-users] Re: choosing force field
Thank you Justin for your kind help. The simple reason for considering only gromos parameter sets is that the parameters for the metal ions (in my protein) are not defined in other force fields. On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012376...@n6.nabble.com wrote: On 11/9/13 12:48 AM, pratibha wrote: Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. 53A6 is known to under-stabilize helices, so if a helix did not appear in a simulation using this force field, it is not definitive proof that the structure does not populate helical structures. I generally see mixed opinions in the literature in terms of which Gromos parameter set is the most reliable. As was asked by someone else, is there a reason you are only considering Gromos parameter sets? Others may be better suited to your study. -Justin On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] [hidden email] http://user/SendEmail.jtp?type=nodenode=5012376i=0 wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: . NAML http://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/choosing-force-field-tp5012242p5012370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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=5012376i=1 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012376i=2 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012376i=3. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012376.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= .
Re: [gmx-users] Re: choosing force field
On 11/9/13 12:48 AM, pratibha wrote: Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. 53A6 is known to under-stabilize helices, so if a helix did not appear in a simulation using this force field, it is not definitive proof that the structure does not populate helical structures. I generally see mixed opinions in the literature in terms of which Gromos parameter set is the most reliable. As was asked by someone else, is there a reason you are only considering Gromos parameter sets? Others may be better suited to your study. -Justin On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5012325...@n6.nabble.com wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012325.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= . 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/choosing-force-field-tp5012242p5012370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Re: choosing force field
Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5012325...@n6.nabble.com wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012325.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= . 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/choosing-force-field-tp5012242p5012370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: choosing force field
My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? Thanks in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012322.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: choosing force field
On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
