My bad, I had a typo, try this one: awk -v x=firstcoordmin -v y=secondcoordmin 'BEGIN{while(getline <"first_coordinate_file_here.xvg"){if($0!~/#/&&$0!~/@/&&$0!~/&/){a[$1]=$2}}}NR>0{if($0!~/#/&&$0!~/@/&&$0!~/&/){if(a[$1]==x&&$2==y){print $1}}}' second_coordinate_file_here.xvg
=================== 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 Naba <nabajyoti.gosw...@gmail.com> Sent: Saturday, August 22, 2015 4:16 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_sham Dear Micholas, The awk command that you have suggested as: awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline < "yourfile_first_coordinate_here.xvg"){if($0!~/#/&&$0!~/@/&&$0!~/&/){a[$1]=$2}}{if($0!~/#/&&$0!~/@/&&$0!~/&/){if(a[$1]==x&&$2==$y){print $1}}' yourfile_second_coordinate_here.xvg is not working. It says "^ unexpected newline or end of string". I have supplied my coord1min, coord2min, yourfile_first_coordinate_here.xvg and yourfile_second_coordinate_here.xvg. can you please re-write the command with correct syntax please? On Fri, Aug 14, 2015 at 10:44 AM, Naba <nabajyoti.gosw...@gmail.com> wrote: > Thank you very much Micholas. > I have actually done the second option. But I was uncertain whether I have > done are all nonsense. > From your replies it seems that I am quite close to fulfill my objectives. > Meanwhile, I am about to perform dPCA for those loops as you have suggested > in the previous mail. > Thanks a lot. > > On Thu, Aug 13, 2015 at 5:32 PM, Smith, Micholas D. <smit...@ornl.gov> > wrote: > >> Hi Naba, >> >> I believe you would want to do your second option if you want to include >> the contributions from all of the loops. If you are just interested in one >> loop, then you would do each seperately. Rule-of-thumb for these >> calculations are whatever group you use for the convariance matrix, is what >> you should use for the 2D projection. >> >> Hope that helps. >> >> >> =================== >> 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 Naba < >> nabajyoti.gosw...@gmail.com> >> Sent: Thursday, August 13, 2015 4:17 AM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] g_sham >> >> Thanks for the reply Micholas. >> >> I read the special discussion on dPCA at your provided link. But that is a >> fact of small peptide penta-alanine. >> I actually completed a 100 ns simulation of a outermembrane protein (of >> 239 >> amino acid residues) with 284 DMPC molecules. The protein contains 4 >> extracellular loops of variable lengths and I want to study the dynamics >> of >> these loops. What I wanted to confirm is: >> >> 1. Is it all right if I extract covariance separately for each loops? OR, >> 2. Should I calculate covariance of index groups of my concerned loops and >> then should I proceed to 2D projection (by g_anaeig)? >> >> >> On Fri, Aug 7, 2015 at 5:50 PM, Smith, Micholas D. <smit...@ornl.gov> >> wrote: >> >> > >1. Is it feasible to obtain free energy landscape (FEL) from a 2D >> > >projection (using g_anaeig) of index groups (say some loop's atoms) >> which >> > >are used for the least squares fit in g_covar and then selecting index >> > >group of elements that corresponds to the eigenvectors (say >> Prot-masses)? >> > >Or, >> > >Should I calculate covariance (g_covar) of my concerned loops >> separately >> > >and then should I go for g_sham? >> > >> > I am not sure if I understand, however, I think I may be able to help a >> > litttle. g_sham is just a histograming program that inverts the >> resulting >> > histogram into energy space, so using a 2D projection is a legitimate >> use. >> > Indeed what you are trying to do is very similar to the steps used in >> dPCA >> > (see: >> > >> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca >> > ). >> > >> > >2. Is there any representative way to get the exact time point for the >> > >corresponding minima obtained from g_sham? >> > >> > If you have the time series for each of the coordinates used in the 2D >> > projection you just need to scan through the 2D timeseries for values >> that >> > match the minimia. e.g. If in the g_sham a minima is at coordinates >> (10,10) >> > than you need to scan through the timeseries of your coordinates: >> > time coord1 coord2 >> > 1 0 0 >> > 2 1 10 >> > 3 40 400 >> > 4 10 25 >> > ....... >> > ....... >> > 5000 10 10 >> > ..... >> > 6000 10 10 >> > ..... >> > 988908 10 10 >> > .... >> > >> > >> > where frames 988908, 5000, and 6000 are the ones you are looking for. >> You >> > could extract these with >> > >> > awk -v x=coord1min -v y=coord2min 'BEGIN{while(getline < >> > >> "yourfile_first_coordinate_here.xvg"){if($0!~/#/&&$0!~/@/&&$0!~/&/){a[$1]=$2}}{if($0!~/#/&&$0!~/@/&&$0!~/&/){if(a[$1]==x&&$2==$y){print >> > $1}}' yourfile_second_coordinate_here.xvg >> > >> > where you would provide the x and y coords of the minina where I have >> > coord1min and coord2min. >> > >> > You may be more interested in getting frames near the minimia and not >> > actually on it, in which case just change the last if-statement as >> needed. >> > >> > Hope that helps. >> > >> > -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 Naba < >> > nabajyoti.gosw...@gmail.com> >> > Sent: Friday, August 07, 2015 12:57 AM >> > To: gromacs.org_gmx-users@maillist.sys.kth.se >> > Subject: [gmx-users] g_sham >> > >> > Dear All, >> > I searched a lot more things about g_sham in the mailing list and >> > eventually getting confused with the inputs. Just make me clear about: >> > >> > 1. Is it feasible to obtain free energy landscape (FEL) from a 2D >> > projection (using g_anaeig) of index groups (say some loop's atoms) >> which >> > are used for the least squares fit in g_covar and then selecting index >> > group of elements that corresponds to the eigenvectors (say >> Prot-masses)? >> > Or, >> > Should I calculate covariance (g_covar) of my concerned loops separately >> > and then should I go for g_sham? >> > >> > 2. Is there any representative way to get the exact time point for the >> > corresponding minima obtained from g_sham? >> > >> > >> > Thanks for all previous helps... >> > Naba >> > >> > Bioinformatics Infrastructure Facility >> > Department of Animal Biotechnology >> > College of Veterinary Science >> > Khanapara,Guwahati 781022 >> > Assam, 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. >> > >> >> >> >> -- >> Nabajyoti Goswami >> >> Research Associate >> Bioinformatics Infrastructure Facility >> Department of Animal Biotechnology >> College of Veterinary Science >> Khanapara,Guwahati 781022 >> Assam, 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. >> > > > > -- > Nabajyoti Goswami > > Research Associate > Bioinformatics Infrastructure Facility > Department of Animal Biotechnology > College of Veterinary Science > Khanapara,Guwahati 781022 > Assam, India > -- Nabajyoti Goswami Research Associate Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, 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.