Re: [gmx-users] Regarding msd
Hi Justin, I get identical results when I use g_msd (should have been clearer at the outset). However, if I extract the coordinates from an unprocessed trajectory with g_traj and run it in my own MSD code, I get different (and wrong) results than if I use -pbc nojump (which ensures a continuous trajectory). Since Pratibha wants to test her own code, the way she treats pbc is something to keep in mind. On Wed, Oct 8, 2014 at 4:59 PM, Justin Lemkul wrote: > > > On 10/8/14 3:21 AM, rajat desikan wrote: > >> Hi, >> You need to use -pbc nojump to calculate the msd. Using -pbc whole is >> wrong >> for calculating the msd. >> >> > Upon what do you base this statement? I get identical results with an > unprocessed trajectory, and those treated with either -pbc whole or -pbc > nojump. > > -Justin > > On Tuesday, October 7, 2014, pratibha kapoor >> wrote: >> >> Hi all >>> >>> I have created my own code for msd calculation and would like to verify >>> it >>> from g_msd. I have created pdb files using trjconv -center -pbc whole >>> option. Can I use the coordinates in pdb as such (with no >>> wrapping/unwrapping/shifting) for running my code? or does the inbuild >>> g_msd program modifies them (shift)? >>> My msd values are not matching with the g_msd values. I suspect that >>> discrepency in the pdb file creation since the values obtained from my >>> program agrees with manual calculation (of some dummy values). >>> Any suggestions are highly welcomed. >>> -- >>> 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 . >>> >>> >> >> > -- > == > > 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 msd
On 10/8/14 3:21 AM, rajat desikan wrote: Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd. Upon what do you base this statement? I get identical results with an unprocessed trajectory, and those treated with either -pbc whole or -pbc nojump. -Justin On Tuesday, October 7, 2014, pratibha kapoor wrote: Hi all I have created my own code for msd calculation and would like to verify it from g_msd. I have created pdb files using trjconv -center -pbc whole option. Can I use the coordinates in pdb as such (with no wrapping/unwrapping/shifting) for running my code? or does the inbuild g_msd program modifies them (shift)? My msd values are not matching with the g_msd values. I suspect that discrepency in the pdb file creation since the values obtained from my program agrees with manual calculation (of some dummy values). Any suggestions are highly welcomed. -- 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 . -- == 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 msd
Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd. On Tuesday, October 7, 2014, pratibha kapoor wrote: > Hi all > > I have created my own code for msd calculation and would like to verify it > from g_msd. I have created pdb files using trjconv -center -pbc whole > option. Can I use the coordinates in pdb as such (with no > wrapping/unwrapping/shifting) for running my code? or does the inbuild > g_msd program modifies them (shift)? > My msd values are not matching with the g_msd values. I suspect that > discrepency in the pdb file creation since the values obtained from my > program agrees with manual calculation (of some dummy values). > Any suggestions are highly welcomed. > -- > 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 msd
Please reply. Its really urgent. I have got comments from reviewer and would have to resubmit the paper. On Tue, Oct 7, 2014 at 10:03 PM, pratibha kapoor wrote: > Hi all > > I have created my own code for msd calculation and would like to verify it > from g_msd. I have created pdb files using trjconv -center -pbc whole > option. Can I use the coordinates in pdb as such (with no > wrapping/unwrapping/shifting) for running my code? or does the inbuild > g_msd program modifies them (shift)? > My msd values are not matching with the g_msd values. I suspect that > discrepency in the pdb file creation since the values obtained from my > program agrees with manual calculation (of some dummy values). > Any suggestions are highly welcomed. > -- 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] Regarding msd
Hi all I have created my own code for msd calculation and would like to verify it from g_msd. I have created pdb files using trjconv -center -pbc whole option. Can I use the coordinates in pdb as such (with no wrapping/unwrapping/shifting) for running my code? or does the inbuild g_msd program modifies them (shift)? My msd values are not matching with the g_msd values. I suspect that discrepency in the pdb file creation since the values obtained from my program agrees with manual calculation (of some dummy values). Any suggestions are highly welcomed. -- 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 MSD
Please reply. Reposting the same query again: I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal wrote: > > > -- Forwarded message -- > From: Nidhi Katyal > Date: Fri, Aug 22, 2014 at 11:41 AM > Subject: Re: regarding MSD > To: Discussion list for GROMACS users > > > Hello > > I have posted the query earlier but havent got any reply and so reposting > it again. > > I have read few papers that determine transition temperature from the plot > of average MSD of hydrogen atoms of protein versus temperature. My question > is: > At a particular temperature, we get a linear curve for MSD versus time, is > it reasonable to calculate average MSD over all such time points? Is this > the average that is plotted in papers (or something is missing) ? My doubt > is won't this average depend on the number of time points (due to its > linear nature)? > > Actually I am trying to reproduce the results of some published data. > Although I am getting the same transition temperature but the MSD values > are coming different (eg at a particular temperature if I average all the > MSD values, I am getting value of 15000 while reported value is 1.5 - both > values in same unit angstrom square) > > Any help is highly appreciated. > > > > On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal > wrote: > >> Hello all >> >> I have read few papers that determine transition temperature from the >> plot of average MSD versus temperature. My question is: >> At a particular temperature, we get a linear curve for MSD versus time, >> is it reasonable to calculate average MSD over all such time points? Is >> this the average that is plotted in papers (or something is missing) ? My >> doubt is won't this average depend on the number of time points (due to its >> linear nature)? >> Any help is highly appreciated. >> >> Thanks >> Nidhi >> > > > -- 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 MSD
Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Actually I am trying to reproduce the results of some published data. Although I am getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) Any help is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal wrote: > Hello all > > I have read few papers that determine transition temperature from the plot > of average MSD versus temperature. My question is: > At a particular temperature, we get a linear curve for MSD versus time, is > it reasonable to calculate average MSD over all such time points? Is this > the average that is plotted in papers (or something is missing) ? My doubt > is won't this average depend on the number of time points (due to its > linear nature)? > Any help is highly appreciated. > > Thanks > Nidhi > -- 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] regarding MSD
Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve for MSD versus time, is it reasonable to calculate average MSD over all such time points? Is this the average that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- 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.
