[gmx-users] Color in wheel
Dear GMX-users, In wheel (helical projection tool), can I make colors for some residues? Besides gray for hydrophobic residues, I also want to make positive charged residues in blue, and negative charged residues in red. Thank you for your help in advance. best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling
Dear GMX-users, I'm simulating lipid bilayer, and since fluctuation is important for the study of undulation and area compressibility (Ka), I'm also applying the Parrinello-Rahman and nose-hoover for the pressure and temperature couplings. When I use the Berendsen, time constants are like below. When I use the PR, do I need to change time constants? Thank you for your time and help in advance. tcoupl = Berendsen ; Groups to couple separately = tc-grps = DPP W ; Time constant (ps) and reference temperature (K) = tau_t = 0.5 0.5 ref_t= 323 323 ; Pressure coupling = Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.2 1.2 compressibility = 5e-5 5e-5 ref_p= 1.0 1.0 -- best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Measure contour area of bilayer undulation
Dear gmx-users, This is not a question about Gromacs, but I wonder if I can hear suggestions from here. I would like to measure contour area of bilayer undulation. If there is no undulation, area (area per lipid) can be easily calculated by dividing XY area by number of lipid. But, in the lipid bilayer with undulation, how can contour area (ultimately, area per lipid) be calculated ? If there are some suggestions about possibilities in Gromacs or other tools, it'd be really appreciated. Thanks, best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to make grids in lipid bilayer (to measure contour length)
Dear gmx-users, I'm trying to calculate contour length of huge lipid bilayer with undulation (non-projected area per lipid). In order to calculate that accurately, I would like to measure contour length in local areas of bilayer by making lots of grids in lipid bilayer. I'm wondering if there is a tool or way to make grids in lipid bilayer in the .xtc trajectories. Thank you for your help in advance. best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about trjorder
Dear GMX-users, I'm using Gromacs 3.3.1, and trying to collect solvents within specific distance from a part of peptide. I typed trjorder -f *.xtc -n *.ndx -s *.tpr -o -nshell -da 8 -na 12 -r 2.5. I correctly typed reference molecule, and the result of -nshell looks OK, but couldn't get the result of -o (.xtc). I wonder if I missed something or there is a bug in trjorder. Thanks for your help. best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculation of the bending modulus (Kc) of bilayer using spectral intensity.
Dear gmx-users, I'm trying to measure the bending modulus (Kc) of lipid bilayer with different sizes. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q, but couldn't understand details. I wonder if I can hear more details and how to do that using GROMACS. Any advice or suggestion will be very appreciated. Thanks, best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: Calculations of area per lipid using g_sas
Dear Mark and David, Thanks for your reply. Dimension of 128-lipid bilayer system is 6.32x6.43x8.57nm, which leads to the projected area/lipid of ~63.5 A^2, and the box size is consistent during whole simulation time. In order to measure total SASA, I typed g_sas -f **.xtc -s **.tpr -o **.xvg -solsize ** with different values of -solsize. Outputs are shown below. Here, my questions is 1) With bigger solvent probes, why does the total SASA decrease ? I thought that SASA should increase because bigger solvents will not insert into the lipid headgroups. 2) with -solsize 1.9, area/lipid can be obtained from 43.0275/2/64=33.6 A^2. How can this be smaller than the projected area/lipid, ~63.5 ? For -solsize 1.5, - # This file was created Tue Jul 10 10:25:24 2007 # by the following command: # g_sas -f test.xtc -s md.tpr -o area0.xvg -solsize 1.5 -b 10 -e 20 # # g_sas is part of G R O M A C S: # # Gnomes, ROck Monsters And Chili Sauce # @title Solvent Accessible Surface @xaxis label Time (ps) @yaxis label Area (nm\S2\N) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv 10 0 85.8878 85.8878 0 100050 0 88.9415 88.9415 0 100100 0 88.0002 88.0002 0 --- For, -solsize 1.7, --- # This file was created Tue Jul 10 10:27:27 2007 # by the following command: # g_sas -f test.xtc -s md.tpr -o area1.xvg -solsize 1.7 -b 10 -e 20 # # g_sas is part of G R O M A C S: # # GRowing Old MAkes el Chrono Sweat # @title Solvent Accessible Surface @xaxis label Time (ps) @yaxis label Area (nm\S2\N) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv 10 0 82.7674 82.7674 0 100050 0 84.0109 84.0109 0 100100 0 85.2114 85.2114 0 - For -solsize 1.9 - This file was created Tue Jul 10 10:28:40 2007 # by the following command: # g_sas -f test.xtc -s md.tpr -o area2.xvg -solsize 1.9 -b 10 -e 20 # # g_sas is part of G R O M A C S: # # Good gRace! Old Maple Actually Chews Slate # @title Solvent Accessible Surface @xaxis label Time (ps) @yaxis label Area (nm\S2\N) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv 10 0 43.0275 43.0275 0 100050 0 47.978 47.978 0 100100 0 38.3633 38.3633 0 -- Thanks, best, Hwankyu. Message: 5 Date: Tue, 10 Jul 2007 15:55:29 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Calculations of area per lipid using g_sas To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hwankyu Lee wrote: [Hide Quoted Text] Dear Mark, I just measured the projected XY-area (simply XY-size of box), and used typical periodic boundary condition (In g_sas, default considers PBC). In the small system (128 lipid bilayer), there is no undulation, so projected area per lipid may be almost the same as non-projected area per lipid. So, total solvent accessible surface area (the third column) should be always larger than the projected XY-area, but I observed that total SASA become smaller than the projected XY-area at some point. Could you give me some suggestions? Show us your box dimensions at a point when you observe this to occur - or preferably a relevant chunk of both g_sas and g_energy output. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Calculations of area per lipid using g_sas
Dear Mark, I just measured the projected XY-area (simply XY-size of box), and used typical periodic boundary condition (In g_sas, default considers PBC). In the small system (128 lipid bilayer), there is no undulation, so projected area per lipid may be almost the same as non-projected area per lipid. So, total solvent accessible surface area (the third column) should be always larger than the projected XY-area, but I observed that total SASA become smaller than the projected XY-area at some point. Could you give me some suggestions? best, Hwankyu. Date: Mon, 9 Jul 2007 10:23:46 +1000 (EST) From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Calculations of area per lipid using g_sas To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=iso-8859-1 [Hide Quoted Text] Dear GMX users, I'm interested in calculating non-projected area/lipid of huge bilayer with undulations. I think that if the bigger solvent probes were used, the non-projected area per lipid may be reasonably calculated from the solvent accessible surface area because solvent probes cannot be inserted between lipid headgroups, which will avoid overestimation of area per lipid. So, I'm testing this with small bilayer (128 lipids) using g_sas, and have some questions. 1) If the bigger solvent probes (such as -solsize 1.7 or so) are used, SASA of lipid will become smaller, but should be always bigger than the XY-area of this small bilayer system. But, when I increased the value of -solsize, SASA becomes even smaller than the XY-area at some point. In this case, how can SASA be smaller than XY-area of the bilayer? How are you measuring XY-area? What periodicity are you using? 2) The manual says that -ndots is related to accuracy, but when I tried different values, I don't see trends of increase or decrease. Could you tell me what it is and what the reasonable value will be? 3) I saw SASA fluctuate quite a lot. Is there any way to decrease fluctuation? Fluctuating with what? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculations of area per lipid using g_sas
Dear GMX users, I'm interested in calculating non-projected area/lipid of huge bilayer with undulations. I think that if the bigger solvent probes were used, the non-projected area per lipid may be reasonably calculated from the solvent accessible surface area because solvent probes cannot be inserted between lipid headgroups, which will avoid overestimation of area per lipid. So, I'm testing this with small bilayer (128 lipids) using g_sas, and have some questions. 1) If the bigger solvent probes (such as -solsize 1.7 or so) are used, SASA of lipid will become smaller, but should be always bigger than the XY-area of this small bilayer system. But, when I increased the value of -solsize, SASA becomes even smaller than the XY-area at some point. In this case, how can SASA be smaller than XY-area of the bilayer? 2) The manual says that -ndots is related to accuracy, but when I tried different values, I don't see trends of increase or decrease. Could you tell me what it is and what the reasonable value will be? 3) I saw SASA fluctuate quite a lot. Is there any way to decrease fluctuation? Thanks for your help in advance. best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Converting CHARMM trajectories (.trj) to GROMACS trajectories (.xtc)
Dear gmx-users, I would like to analyze CHARMM trajectories in GROMACS, and wonder if there are available scripts or tools to convert CHARMM traj to GROMACS traj (.xtc). I've searched the contributed software and forum sections, and it looks like there is a script for that, but couldn't find it. If you can provide me scripts for that, it'll be appreciated. Thanks, best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf
Dear Gromacs-users, I would like to use the analysis tool g_sdf, but couldn't find in the download section. If someone has the file, would you like to send me that ? Does it work with gromacs-3.3.1? Thank you very much for your help in advance. best, Hwankyu. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
