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 wit

[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-tp499969

[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 takin

[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

[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-

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

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 abou

[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 bon

Re: [gmx-users] h-bonds constraints

Thanks! That's reasonable. On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu wrote: > On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban > 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. > >

Re: [gmx-users] h-bonds constraints

On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban 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

[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 lis

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 did

[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

[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.