[gmx-users] Regarding the comparison of two result
Dear Friends, I did MD simulation of two peptide that show that they form antiparallel beta sheet structure after 120 ns . i used gromacs 4.5.5 version. presently I completed MD simulation of another peptide ( Different sequence). but I am using gromacs 4.6.3 . I found that two peptide start to form anti parallelstructure around 15 ns. My question is that are this two result at all comparable as the version of software is diff. ?? is this result upto publication ??? I am looking forward for answer . I know this is a very simple but complicated to me. With best wishes, Rama David -- 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] Regarding the comparison of two result
On 5/2/14, 1:37 AM, rama david wrote: Dear Friends, I did MD simulation of two peptide that show that they form antiparallel beta sheet structure after 120 ns . i used gromacs 4.5.5 version. presently I completed MD simulation of another peptide ( Different sequence). but I am using gromacs 4.6.3 . I found that two peptide start to form anti parallelstructure around 15 ns. My question is that are this two result at all comparable as the version of software is diff. ?? is this result upto publication ??? I am looking forward for answer . I know this is a very simple but complicated to me. You'd have to look into the release notes to see if there were any relevant changes based on your run settings and such. There were hundreds of changes between 4.5.5 and 4.6.3 - changing between release series can be a bit dicey. Changes within a release series should give consistent results, except in the case of critical bugs being fixed (i.e. everything in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and 4.6.x may not necessarily be the same, depending on what the relevant changes were). I would expect "standard" MD to probably be OK, but you really do need to look at all of the changes to determine if that's right. Rule of thumb (at least, in my mind) - pick a version (the newest one available at the time, or whatever makes sense for scientific continuity with other ongoing or completed work) and stick with it. -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 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] Regarding the comparison of two result
Hi, I would suggest caution. I had a DPPC bilayer interacting with organic molecules (beta naphthol) which are supposed to alter the phase behaviour. The initial simulations using group cutoffs didn't capture one region of the experimental phase diagram, even with 200 ns of simulation (SLIPIDS + GAFF). However, I am able to capture this phase with Verlet cutoffs in version 4.6.4 in the high temperature range (Low temperature is problematic due to kinetic trapping in all simulations). This is probably because the Verlet cutoff scheme uses better model physics. So, make a cautious decision before going ahead. Regards, On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul wrote: > > > On 5/2/14, 1:37 AM, rama david wrote: > >> Dear Friends, >> >> I did MD simulation of two peptide that show that they form antiparallel >> beta sheet structure after 120 ns . i used gromacs 4.5.5 version. >> presently I completed MD simulation of another peptide >> ( >> Different sequence). but I am using gromacs 4.6.3 . I found that two >> peptide start to form anti parallelstructure around 15 ns. >>My question is that are this two result at all comparable >> as >> the version of software is diff. ?? is this result upto publication ??? >> >> >> I am looking forward for answer . >> I know this is a very simple but complicated to me. >> >> > You'd have to look into the release notes to see if there were any > relevant changes based on your run settings and such. There were hundreds > of changes between 4.5.5 and 4.6.3 - changing between release series can be > a bit dicey. Changes within a release series should give consistent > results, except in the case of critical bugs being fixed (i.e. everything > in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and > 4.6.x may not necessarily be the same, depending on what the relevant > changes were). I would expect "standard" MD to probably be OK, but you > really do need to look at all of the changes to determine if that's right. > Rule of thumb (at least, in my mind) - pick a version (the newest one > available at the time, or whatever makes sense for scientific continuity > with other ongoing or completed work) and stick with it. > > -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 > > 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. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding the comparison of two result
I forgot to mention that the earlier simulations were with version 4.5.4 On Fri, May 2, 2014 at 6:13 PM, rajat desikan wrote: > Hi, > I would suggest caution. I had a DPPC bilayer interacting with organic > molecules (beta naphthol) which are supposed to alter the phase behaviour. > The initial simulations using group cutoffs didn't capture one region of > the experimental phase diagram, even with 200 ns of simulation (SLIPIDS + > GAFF). However, I am able to capture this phase with Verlet cutoffs in > version 4.6.4 in the high temperature range (Low temperature is problematic > due to kinetic trapping in all simulations). This is probably because the > Verlet cutoff scheme uses better model physics. So, make a cautious > decision before going ahead. > > Regards, > > > On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul wrote: > >> >> >> On 5/2/14, 1:37 AM, rama david wrote: >> >>> Dear Friends, >>> >>> I did MD simulation of two peptide that show that they form >>> antiparallel >>> beta sheet structure after 120 ns . i used gromacs 4.5.5 version. >>> presently I completed MD simulation of another >>> peptide ( >>> Different sequence). but I am using gromacs 4.6.3 . I found that two >>> peptide start to form anti parallelstructure around 15 ns. >>>My question is that are this two result at all comparable >>> as >>> the version of software is diff. ?? is this result upto publication ??? >>> >>> >>> I am looking forward for answer . >>> I know this is a very simple but complicated to me. >>> >>> >> You'd have to look into the release notes to see if there were any >> relevant changes based on your run settings and such. There were hundreds >> of changes between 4.5.5 and 4.6.3 - changing between release series can be >> a bit dicey. Changes within a release series should give consistent >> results, except in the case of critical bugs being fixed (i.e. everything >> in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and >> 4.6.x may not necessarily be the same, depending on what the relevant >> changes were). I would expect "standard" MD to probably be OK, but you >> really do need to look at all of the changes to determine if that's right. >> Rule of thumb (at least, in my mind) - pick a version (the newest one >> available at the time, or whatever makes sense for scientific continuity >> with other ongoing or completed work) and stick with it. >> >> -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 >> >> 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. >> > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding the comparison of two result
Dear friends, Thank you Justin and Rajat for your suggestions. I think it is really better to do all the MD in latest version or in the same version. That will avoid the unnecessary falls and critics. With best regards, Rama david On Fri, May 2, 2014 at 6:13 PM, rajat desikan wrote: > I forgot to mention that the earlier simulations were with version 4.5.4 > > > On Fri, May 2, 2014 at 6:13 PM, rajat desikan >wrote: > > > Hi, > > I would suggest caution. I had a DPPC bilayer interacting with organic > > molecules (beta naphthol) which are supposed to alter the phase > behaviour. > > The initial simulations using group cutoffs didn't capture one region of > > the experimental phase diagram, even with 200 ns of simulation (SLIPIDS + > > GAFF). However, I am able to capture this phase with Verlet cutoffs in > > version 4.6.4 in the high temperature range (Low temperature is > problematic > > due to kinetic trapping in all simulations). This is probably because the > > Verlet cutoff scheme uses better model physics. So, make a cautious > > decision before going ahead. > > > > Regards, > > > > > > On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul wrote: > > > >> > >> > >> On 5/2/14, 1:37 AM, rama david wrote: > >> > >>> Dear Friends, > >>> > >>> I did MD simulation of two peptide that show that they form > >>> antiparallel > >>> beta sheet structure after 120 ns . i used gromacs 4.5.5 version. > >>> presently I completed MD simulation of another > >>> peptide ( > >>> Different sequence). but I am using gromacs 4.6.3 . I found that two > >>> peptide start to form anti parallelstructure around 15 ns. > >>>My question is that are this two result at all > comparable > >>> as > >>> the version of software is diff. ?? is this result upto publication ??? > >>> > >>> > >>> I am looking forward for answer . > >>> I know this is a very simple but complicated to me. > >>> > >>> > >> You'd have to look into the release notes to see if there were any > >> relevant changes based on your run settings and such. There were > hundreds > >> of changes between 4.5.5 and 4.6.3 - changing between release series > can be > >> a bit dicey. Changes within a release series should give consistent > >> results, except in the case of critical bugs being fixed (i.e. > everything > >> in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and > >> 4.6.x may not necessarily be the same, depending on what the relevant > >> changes were). I would expect "standard" MD to probably be OK, but you > >> really do need to look at all of the changes to determine if that's > right. > >> Rule of thumb (at least, in my mind) - pick a version (the newest one > >> available at the time, or whatever makes sense for scientific continuity > >> with other ongoing or completed work) and stick with it. > >> > >> -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 > >> > >> 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. > >> > > > > > > > > -- > > Rajat Desikan (Ph.D Scholar) > > Prof. K. Ganapathy Ayappa's Lab (no 13), > > Dept. of Chemical Engineering, > > Indian Institute of Science, Bangalore > > > > > > -- > Rajat Desikan (Ph.D Scholar) > Prof. K. Ganapathy Ayappa's Lab (no 13), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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.
