[gmx-users] H-bonds per molecule across the box
Dear Gromacs users, Is it easily possible to calculate the number of H-bonds per molecule across the box by using gromacs? If it is, how can I do this? Thanks in advance, Akn. -- View this message in context: http://gromacs.5086.n6.nabble.com/H-bonds-per-molecule-across-the-box-tp4999698.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] H-bonds per molecule across the box
On 7/26/12 6:23 AM, akn wrote: Dear Gromacs users, Is it easily possible to calculate the number of H-bonds per molecule across the box by using gromacs? If it is, how can I do this? One would have to use g_select on a particular region of the box (simple coordinate boundaries) to work with atoms in that region. The result is an index file for each frame in the trajectory. You must then loop over all these index groups (which may be of different size in each frame) and conduct analysis using a for-loop in a shell script (or something similar) since there is no automatic way to use the index files produced by g_select in this case. See the discussion on this topic from last week in the archive. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] H-bonds
Hi everyone! I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am taking advantage of the hbmap file to parse out the Hbond trajectories needed to count the water bridges. A possible water-bridge type is one in which the hydrogen of a water molecule is shared by two different oxygens of the solute. Since there are two H's per water molecule I expected two sets of indices for each H. This is what I did. 1. To simplify parsing the resulting HBMap, I intended to create an HBMap.xpm for a water and a pair of hydroxyl residues from the solute. For a shared H above, that would be (O solute...Hwater...O solute). Creating a set of indices for this configuration was successful upon running (g_hbond -hbn), but only for one set of Hwater. g_hbond was not able to create another set for the other H of water. (Note though that g_hbond was able to correctly identify both Hs of water as donors). g_hbond correctly counted H-bonds for this set and produced a reliable HBMap.xpm 2. Another set of indices was manually created for the other H. However, the hbnum.xvg of this set is unreliable compared with the above and the values shoot to 1000 times expected h-bond counts. Please note that the HBMap.xpm for the hydrogen bonds between water and the solute only lists one H for each water as if ignoring the other H (in cases that there should be two). Your advice/ideas/comments is very much welcome and very much needed. Thanks, Bernard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] h-bonds constraints for DPPC sim?
Hi It was mentioned here http://lists.gromacs.org/pipermail/gmx-users/2011-May/061475.html that the constraints option may have to be set to h-bonds to get the exp APL in DPPC equilibration/simulation. Is this indeed true and if so how important is it for membrane/protein simulations? Thanks in advance. George -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] h-bonds constraints
Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] H bonds
Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) is there a way to get residues engaged in the bond (with occupancy rate if possible) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] H bonds
larif sofiene wrote: Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. Have you tried using an index group that specifies the residue of interest? When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) The index file produced with the -hbn flag maps to the existence matrix in hbmap.xpm. -Justin is there a way to get residues engaged in the bond (with occupancy rate if possible) -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] H bonds
Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) You can check the bonds index created by g_hbond -hbn . -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] h-bonds constraints
What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] h-bonds constraints
On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote: What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. Any atom name starting with H or h (so case-insensitive). Cheers, Bogdan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] h-bonds constraints
Thanks! That's reasonable. On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu bcoste...@gmail.com wrote: On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote: What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. Any atom name starting with H or h (so case-insensitive). Cheers, Bogdan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] H-bonds
Hi, please I'm trying to measure an hbond between 2 specific atoms. When I used g_hbond I didn't the result I expected because it doesn't specify the atoms that constitute the H bond. Now I'm trying with g_dist but I encountered a problem: when I do the following in my index file: r 172 a HD2 it tells me: empty group So please can anyone help me? Thank you. Carla -- 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] H-bonds
Carla Jamous wrote: Hi, please I'm trying to measure an hbond between 2 specific atoms. When I You won't be able to. A hydrogen bond is defined as occurring between 3 atoms (D-H...A) for geometric reasons, so you have to specify at least three atoms for the analysis. used g_hbond I didn't the result I expected because it doesn't specify the atoms that constitute the H bond. Now I'm trying with g_dist but I encountered a problem: when I do the following in my index file: r 172 a HD2 it tells me: empty group Apparently there is no atom named HD2 in residue 172. Be sure you're analyzing the right residue. -Jusitn So please can anyone help me? Thank you. Carla -- 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] H-bonds in water + alcohol mixture
Dear all, I'm trying to evaluate the number of H-bonds in a 150 alcohol (TraPPE) + 57 water (SPC/E) molecules mixture. From rdf analysis I can observe that the most prominent peak is related to OW-OW group, followed by OW-OH group and finally OH-OH group. OW = water oxygen OH = alcohol oxygen. From g_hbond analysis I have calculated (at fixed cutoff = 0.35 nm + angle = 30ยบ) the following average number of hydrogen bonds per time step: Water - Water = 36.53 -- 36.53 / 57= 0.64 per molecule Water - Alcohol = 106.13 -- 106.13/207 = 0.513 Alcohol - Alcohol = 96.23 -- 96.23/150= 0.64 I was expected to observe the same trend in both rdf and number of H-bonds... Someone has some clue about what I am doing wrong ? Thanks in advance Nuno Garrido -- 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
