Re: [gmx-users] Force-field bias???
On Wed, 5 Aug 2015, Justin Lemkul wrote: On 8/5/15 10:32 AM, Smith, Micholas D. wrote: OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppose to take a while to fold. If you just want to get to the folded structure, and you don't care about the pathway, you could also use an enhanced sampling technique. An alternative force-field that seems to handle beta structures pretty well, but can sometime accelerate the folding is the older GROMOS53A force-field; though since it is united atom, I have found that sometime the contacts don't quite match with NMR data. Beware, it's well known that 53A6 systematically under-stabilizes helices such that you get inappropriate unfolding. It samples the unfolded state quite well, but again, this may be application-specific. That under-stabilization of helices in 53A6 seems to have been mostly solved by the few changes that led to 54A7, which is able to reproduce both the thermodynamics and the kinetics of helix formation in a cyclic peptide model (doi: 10.1021/ct400529k). So, I would say that 54A7 is largely a fixed 53A6 in that respect (plus a few changes on choline groups and ions). Of course, the fact that the kinetics seems good is not necessarily a good thing if you just want thermodynamics (relative populations), because sampling may turn out to be too slow for your system... or not... Best, Antonio -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- -Justin Force-field choice is a non-trival, but largely difficult problem to deal with. In general, though, I tend to avoid the older Amber force-fields when simulating beta-rich peptides as have had a bias towards helical structures (see the references within the paper I noted above). Good Luck, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin tetramer protein that comprises largely of beta strands, and I have used the OPLS ff, so far I have not been successful, can OPLS be a problem at all?? Thanks.. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. smit...@ornl.gov wrote: You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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
Re: [gmx-users] Force-field bias???
Thank you Justin, Vitaly. Thank you @Micholas, the paper you referred is helping me clear many of my queries. I will continue to look for answers keeping your valuable comments in mind. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 10:39 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/5/15 10:32 AM, Smith, Micholas D. wrote: OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppose to take a while to fold. If you just want to get to the folded structure, and you don't care about the pathway, you could also use an enhanced sampling technique. An alternative force-field that seems to handle beta structures pretty well, but can sometime accelerate the folding is the older GROMOS53A force-field; though since it is united atom, I have found that sometime the contacts don't quite match with NMR data. Beware, it's well known that 53A6 systematically under-stabilizes helices such that you get inappropriate unfolding. It samples the unfolded state quite well, but again, this may be application-specific. -Justin Force-field choice is a non-trival, but largely difficult problem to deal with. In general, though, I tend to avoid the older Amber force-fields when simulating beta-rich peptides as have had a bias towards helical structures (see the references within the paper I noted above). Good Luck, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin tetramer protein that comprises largely of beta strands, and I have used the OPLS ff, so far I have not been successful, can OPLS be a problem at all?? Thanks.. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. smit...@ornl.gov wrote: You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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. -- 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
[gmx-users] Force-field bias???
Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. I am new to this field, I would like your generous help. Thanks in advance. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, 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.
Re: [gmx-users] Force-field bias???
I believe, yes, it can. Dihedrals can make a big difference... On Wed, Aug 5, 2015 at 7:24 AM, SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. I am new to this field, I would like your generous help. Thanks in advance. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, 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. -- 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] Force-field bias???
On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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] Force-field bias???
You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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. -- 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] Force-field bias???
Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin tetramer protein that comprises largely of beta strands, and I have used the OPLS ff, so far I have not been successful, can OPLS be a problem at all?? Thanks.. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. smit...@ornl.gov wrote: You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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. -- 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. -- 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] Force-field bias???
OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppose to take a while to fold. If you just want to get to the folded structure, and you don't care about the pathway, you could also use an enhanced sampling technique. An alternative force-field that seems to handle beta structures pretty well, but can sometime accelerate the folding is the older GROMOS53A force-field; though since it is united atom, I have found that sometime the contacts don't quite match with NMR data. Force-field choice is a non-trival, but largely difficult problem to deal with. In general, though, I tend to avoid the older Amber force-fields when simulating beta-rich peptides as have had a bias towards helical structures (see the references within the paper I noted above). Good Luck, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin tetramer protein that comprises largely of beta strands, and I have used the OPLS ff, so far I have not been successful, can OPLS be a problem at all?? Thanks.. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. smit...@ornl.gov wrote: You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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. -- 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. -- 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post
Re: [gmx-users] Force-field bias???
On 8/5/15 10:32 AM, Smith, Micholas D. wrote: OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppose to take a while to fold. If you just want to get to the folded structure, and you don't care about the pathway, you could also use an enhanced sampling technique. An alternative force-field that seems to handle beta structures pretty well, but can sometime accelerate the folding is the older GROMOS53A force-field; though since it is united atom, I have found that sometime the contacts don't quite match with NMR data. Beware, it's well known that 53A6 systematically under-stabilizes helices such that you get inappropriate unfolding. It samples the unfolded state quite well, but again, this may be application-specific. -Justin Force-field choice is a non-trival, but largely difficult problem to deal with. In general, though, I tend to avoid the older Amber force-fields when simulating beta-rich peptides as have had a bias towards helical structures (see the references within the paper I noted above). Good Luck, Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin tetramer protein that comprises largely of beta strands, and I have used the OPLS ff, so far I have not been successful, can OPLS be a problem at all?? Thanks.. Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. smit...@ornl.gov wrote: You should also note that force-field bias may be system dependent. So if you are unsure of the dynamics from the onset, you should likely test a variety of force-fields and/or try to find a comparison to NMR (or other) experimental methods. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how this may happen. Yes, this is true. It usually comes down to errors in the balance between intra-protein and protein-water interactions. Incorrect balance favors either the folded or unfolded state. No force field is perfect, but some are better than others and there's lots of literature on this topic regarding which are the most successful. -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. -- 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. -- 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
