Re: [gmx-users] Unstable Alpha Helix
Hi, Yes of course lots of mdp parameters affect the quality of your model physics. You should choose them carefully, in particular to align with how your force field was parameterized, or is subsequently used (and shown to work well). Offhand, the AMBER force fields are paramterized and used plain cutoff VDW, so your use of potential-switch implements a model that is at best doubtful until shown otherwise. Mark On Wed, Dec 21, 2016 at 9:16 PM <amitbe...@chemeng.iisc.ernet.in> wrote: > Hello Justin, > I am using "stride" program to analyze the helices. > Can the Potential switch and other mdp parameters affect the stability of > an Alphahelix. > > Regards, > Amit > > Date: Mon, 19 Dec 2016 08:06:29 -0500 > > From: Justin Lemkul <jalem...@vt.edu> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Unstable Alpha Helix > > Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c...@vt.edu> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > > > On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote: > >> Hello everyone, > >> I am trying to simulate an Alpha helix inside a bilayer. But a part of > >> the > >> alpha helix is loosing its form and converting into turns( while > >> alphahelix should be stable in the bilayer environment) > > > > How are you assessing this? DSSP? Dihedral time series? Note that > > simple > > visualization is often misleading. Helices can still be helices, even if > > the > > program you're looking at disagrees. > > > > -Justin > > > >> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. > >> I am using Potential-switch for VdW and PME for electrostatics. > >> Does these parameters affect the form of the Alphahelix ? > >> > >> Regards, > >> Amit > >> > > > > -- > > == > > > > 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] Unstable Alpha Helix
Hello Justin, I am using "stride" program to analyze the helices. Can the Potential switch and other mdp parameters affect the stability of an Alphahelix. Regards, Amit > Date: Mon, 19 Dec 2016 08:06:29 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Unstable Alpha Helix > Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote: >> Hello everyone, >> I am trying to simulate an Alpha helix inside a bilayer. But a part of >> the >> alpha helix is loosing its form and converting into turns( while >> alphahelix should be stable in the bilayer environment) > > How are you assessing this? DSSP? Dihedral time series? Note that > simple > visualization is often misleading. Helices can still be helices, even if > the > program you're looking at disagrees. > > -Justin > >> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. >> I am using Potential-switch for VdW and PME for electrostatics. >> Does these parameters affect the form of the Alphahelix ? >> >> Regards, >> Amit >> > > -- > == > > 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] Unstable Alpha Helix
On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello everyone, I am trying to simulate an Alpha helix inside a bilayer. But a part of the alpha helix is loosing its form and converting into turns( while alphahelix should be stable in the bilayer environment) How are you assessing this? DSSP? Dihedral time series? Note that simple visualization is often misleading. Helices can still be helices, even if the program you're looking at disagrees. -Justin I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. I am using Potential-switch for VdW and PME for electrostatics. Does these parameters affect the form of the Alphahelix ? Regards, Amit -- == 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] Unstable Alpha Helix
Hello everyone, I am trying to simulate an Alpha helix inside a bilayer. But a part of the alpha helix is loosing its form and converting into turns( while alphahelix should be stable in the bilayer environment) I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. I am using Potential-switch for VdW and PME for electrostatics. Does these parameters affect the form of the Alphahelix ? Regards, Amit -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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.
