[gmx-users] intrapeptide hbond existence map
Ok thank you all for your suggestions A bientot > > ABEL Stephane 175950 wrote: >> Hi everybody, >> I am doing some analysis of the interpeptidique hbonds (INTRHB) >> during the aggregation in beta fuof 4 heptapeptides in water >> I have defined in a index file the Acceptor-Donor-Hydrogen atoms list >> for the 28 INTRHB like this >> NH--CO >> >> >> [intra_hbds] >> 4 17 5 >> 18 26 19 >> 27 43 28 >> 44 52 45 >> 53 60 54 >> >> >> to obtain the INTRHB existence map i used the command with gmx4.05 >> >> g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f >> ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn >> 4_Peptide_53A6_hbonds_400_500ns_index -hbm >> 4_Peptide_53A6_hbonds_400_500ns_Map >> >> The map show in the x and y axis the time and residue (up to 84). I >> have no idea what the figure means. The olot is stored here >> http://www.st-abel.com/Hbond_occupency.jpg >> >> I want only to know if, for example, the Hbond_occupency for the >> group NH or CO of the residu 1 > > The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the > donor-acceptor pairs to the plot. Find within that index file a > directive that starts with "hbonds" that corresponds to all of the > H-bonds that were found, and thus plotted. Red indicates the H-bond > exists, white means it doesn't. As for occupancy, you'd probably have > to script that to parse the .xpm file and calculate a percentage of > frames for when the particular H-bond exists, or get lifetimes from > g_hbond. > > -Justin .or to define smaller index groups, e.g. the NH- or CO-group of res 1, and get the number of hydrogen bonds as function of time from the -num output (default is hbnum.xvg). You would have to repeat this for all (reasonable combinations of) hbonding groups that you're interested in, which can result in maaany g_hbond executions. But if the number of groups are small, then it's certainly doable. It seems from your plot though, that scripted processing of the -hbm and -hbn output, as Justin suggests, is the way to go here. Make sure you're matching the index file to the xpm file in the right way! I've made mistakes in that area myself. Erik > >> Thank you in advance for your help >> >> Stephane >> >> >> >> >> >> >> > -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- Message: 5 Date: Thu, 11 Feb 2010 09:49:42 -0800 From: Lum Nforbi Subject: [gmx-users] Working with Reduced Units To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi all, Please, can someone shed more light on how to set up reduced units in an .mdp file? I have tried to this but it does not work. I set epsilon, sigma and mass to 1 in my force field file as stated in section 2.3 of the manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon to get a temperature in reduced units with value 2.5. I also calculated the pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get a value of 0.0431 and included all of these in the .mdp file but this did not work for me in the mdrun. Is this the right way to set up reduced units in gromacs? Please, help me out. Thanks, Lum -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100211/890182c2/attachment-0001.html -- Message: 6 Date: Thu, 11 Feb 2010 18:40:10 + From: Rebeca Garc?a Fandi?o Subject: [gmx-users] different results in different machines To: Message-ID: Content-Type: text/plain; charset="iso-8859-1" Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: comparation_neuron_ngs.pdf Type: application/pdf Size: 3110 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20100211/efa9e0c0/comparation_neuron_ngs.pdf -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 70, Issue 75 * <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intrapeptide hbond existence map
Justin A. Lemkul skrev: ABEL Stephane 175950 wrote: Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the donor-acceptor pairs to the plot. Find within that index file a directive that starts with "hbonds" that corresponds to all of the H-bonds that were found, and thus plotted. Red indicates the H-bond exists, white means it doesn't. As for occupancy, you'd probably have to script that to parse the .xpm file and calculate a percentage of frames for when the particular H-bond exists, or get lifetimes from g_hbond. -Justin …or to define smaller index groups, e.g. the NH- or CO-group of res 1, and get the number of hydrogen bonds as function of time from the -num output (default is hbnum.xvg). You would have to repeat this for all (reasonable combinations of) hbonding groups that you're interested in, which can result in maaany g_hbond executions. But if the number of groups are small, then it's certainly doable. It seems from your plot though, that scripted processing of the -hbm and -hbn output, as Justin suggests, is the way to go here. Make sure you're matching the index file to the xpm file in the right way! I've made mistakes in that area myself. Erik Thank you in advance for your help Stephane -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intrapeptide hbond existence map
Hi Stephane, The map shows weather a certain hydrogen bond exists at a certain time. In principle you can get the information by integrating this data, but I'm not sure it can be done without changing the code. A possible solution is to use a script and run g_hbond -num 28 times with two relevant groups (N-H donor and oxygen acceptor), and calculate the occupancy based on this (I guess you mean the fraction of time that this h_bond existed. Ran. ABEL Stephane 175950 wrote: > Hi everybody, > > I am doing some analysis of the interpeptidique hbonds (INTRHB) during the > aggregation in beta fuof 4 heptapeptides in water > > I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the > 28 INTRHB like this > > NH--CO > > > [intra_hbds] > 4 17 5 > 18 26 19 > 27 43 28 > 44 52 45 > 53 60 54 > > > to obtain the INTRHB existence map i used the command with gmx4.05 > > g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f > ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn > 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map > > The map show in the x and y axis the time and residue (up to 84). I have no > idea what the figure means. The olot is stored here > http://www.st-abel.com/Hbond_occupency.jpg > > I want only to know if, for example, the Hbond_occupency for the group NH or > CO of the residu 1 > > Thank you in advance for your help > > Stephane > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intrapeptide hbond existence map
ABEL Stephane 175950 wrote: Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the donor-acceptor pairs to the plot. Find within that index file a directive that starts with "hbonds" that corresponds to all of the H-bonds that were found, and thus plotted. Red indicates the H-bond exists, white means it doesn't. As for occupancy, you'd probably have to script that to parse the .xpm file and calculate a percentage of frames for when the particular H-bond exists, or get lifetimes from g_hbond. -Justin Thank you in advance for your help Stephane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intrapeptide hbond existence map
Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 Thank you in advance for your help Stephane <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
