Re: [gmx-users] g_hbond problems

On 3/10/17 4:51 AM, andrea.cor...@unina.it wrote: I am trying to analyze the hydrogen bonds of my simulations by g_hbond. I am using an index file where I created two groups: one with acceptor atoms (carboxylic oxygen atoms in my structure) and another group with the water molecules. I got

[gmx-users] g_hbond problems

I am trying to analyze the hydrogen bonds of my simulations by g_hbond. I am using an index file where I created two groups: one with acceptor atoms (carboxylic oxygen atoms in my structure) and another group with the water molecules. I got a segmentation fault with the message: Select

Re: [gmx-users] g_hbond: range checking error

Hi.. Thanks for the reply. I was unable to download gromacs-5.1.2; when i clicked on the link, it showed "the site can't be reached." However I have been able to figure out the solution. The trajectory file I was using for analysis of protein-solvent hydrogen bonds did not contain water

Re: [gmx-users] g_hbond: range checking error

Hi, Strange. Do you get the same error with 5.1.2? If so, can you please file a redmine issue (http://redmine.gromacs.org/) and upload the input files that generate this error? Assign the issue to me. Kind regards Erik Marklund On 26 Apr 2016, at 12:01, Shubhangi Gupta

[gmx-users] g_hbond: range checking error

Hi all, I want to calculate the number of hydrogen bonds between protein and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups - protein and SOL. When i run the command, I get a *Range Checking error* *Variable gx has value -3. It should have been within [0 ..19]*

[gmx-users] g_hbond

Dear all I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file. Then with xpm2ps I converted .xpm to .eps file. I get half the number of rows in .eps file as compared to .ndx file. when using Justins perl script I got summary of existence file and here 12 bonds are shown but in

Re: [gmx-users] g_hbond

On 9/11/15 2:43 AM, Shahid Nayeem wrote: Dear all I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file. Then with xpm2ps I converted .xpm to .eps file. I get half the number of rows in .eps file as compared to .ndx file. when using Justins perl script I got summary of

[gmx-users] g_hbond

Dear all I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file. Then with xpm2ps I converted .xpm to .eps file. I get half the number of rows in .eps file as compared to .ndx file. when using Justins perl script I got summary of existence file and here 12 bonds are shown but in

[gmx-users] g_hbond

Hello, I'm trying to use g_hbond to calculate H-bonds between two different species, but it seems to be counting the donor atom as an acceptor as well. e.g. instead of measuring the H-bonds of water to acetate oxygens, it seems to be measuring the H-bonds of water to acetate oxygens and water

Re: [gmx-users] g_hbond

On 8/4/15 9:40 AM, jwill...@andrew.cmu.edu wrote: Hello, I'm trying to use g_hbond to calculate H-bonds between two different species, but it seems to be counting the donor atom as an acceptor as well. e.g. instead of measuring the H-bonds of water to acetate oxygens, it seems to be

Re: [gmx-users] g_hbond : normalization autocorrelation function.

On 7/19/15 10:55 AM, Nilesh Dhumal wrote: Erik, I want autocorrelation function without normalization. Use the -nonormalize option. -Justin Exact value at t=0, t=1 is with normalization. Nilesh Hi Nilesh, I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What

Re: [gmx-users] g_hbond : normalization autocorrelation function.

Erik, I want autocorrelation function without normalization. Exact value at t=0, t=1 is with normalization. Nilesh Hi Nilesh, I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What normalisation do you expect? Kind regards, Erik Erik Marklund, PhD Postdoctoral

Re: [gmx-users] g_hbond : normalization autocorrelation function.

Hi Nilesh, I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What normalisation do you expect? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of

[gmx-users] g_hbond : normalization autocorrelation function.

Hello, I am calculating autocorrelation function without normalization using g_hbond g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac ./test/hbac_3.xvg -num ./test/num_3.xvg The output, hbac_3.xvg, don't have normalized auto correlation function. Here is initial part @title

Re: [gmx-users] g_hbond

Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?

Re: [gmx-users] g_hbond

Hello Erik, I did the same. Thanks, Nilesh Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I

Re: [gmx-users] g_hbond

I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? Nilesh But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik On 10 Jul 2015, at 15:17, Nilesh Dhumal

Re: [gmx-users] g_hbond

But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032

Re: [gmx-users] g_hbond

I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is

Re: [gmx-users] g_hbond

This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many

Re: [gmx-users] g_hbond

Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between

[gmx-users] g_hbond

Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? Default -r cutoff is 0.35nm. Is the distance

Re: [gmx-users] g_hbond

Thanks. I will use two groups. Nilesh On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)?

Re: [gmx-users] g_hbond

On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)?

Re: [gmx-users] g_hbond

On 7/9/15 9:13 PM, Nilesh Dhumal wrote: On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group

Re: [gmx-users] g_hbond

On 7/9/15 9:02 PM, Nilesh Dhumal wrote: Hello, I am calculating g_hbond for water system. I have a question about specifying two group for calculating hydrogen bond. Do I specify atoms in triplet(O-H---O)? Can I specify O-H as one group (Donor-Hydrogen) and O in other group (Acceptor)? If

[gmx-users] g_hbond on trajectory

Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg The log file showed me:

Re: [gmx-users] g_hbond on trajectory

On 6/2/15 5:01 AM, Jennifer Vo wrote: Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist

Re: [gmx-users] g_hbond on trajectory

Thank you, Justin. Jennifer On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/2/15 5:01 AM, Jennifer Vo wrote: Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s

[gmx-users] g_hbond never shows hbond with HW2

Dear list, I discovered something strange today. In my hbond search i find only HW1 of the water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ donors_hydrogens_Water ] entry in the ndx file. So

Re: [gmx-users] g_hbond never shows hbond with HW2

On 5/1/15 11:27 AM, Ebert Maximilian wrote: Dear list, I discovered something strange today. In my hbond search i find only HW1 of the water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to the fact that I am using SPC water? I can see the atom IDs of HW2 in the [

Re: [gmx-users] g_hbond not running

To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Date: Wed, 17 Dec 2014 09:15:41 + Subject: Re: [gmx-users] g_hbond not running Hi Tony, Would you mind sending me the tpr and trr off list so I can have a closer look and maybe debug? Erik On 17 Dec 2014, at 09:10, antoni borysik

Re: [gmx-users] g_hbond not running

Hi Erik - yes tried that and no luck. g_hbond runs well with with some simulation but not others. Can't figure it out, or why no-one has come across this one before. From: erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org Date: Tue, 16 Dec 2014 14:50:15 + Subject: Re: [gmx-users

Re: [gmx-users] g_hbond not running

will do thanks a lot. Toni From: erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org Date: Wed, 17 Dec 2014 09:15:41 + Subject: Re: [gmx-users] g_hbond not running Hi Tony, Would you mind sending me the tpr and trr off list so I can have a closer look and maybe debug? Erik

Re: [gmx-users] g_hbond not running

a lot. Toni From: erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Date: Wed, 17 Dec 2014 09:15:41 + Subject: Re: [gmx-users] g_hbond not running Hi Tony, Would you mind sending me the tpr and trr off list so I can have

[gmx-users] g_hbond not running

Hi, have run various vacuum simulations with GROMACS 4.6.7. I find I can calculate h-bonds using g_hbond -f md.trr -s md.tpr on some simulations just fine while on others the system freezes 'Frame loop parallelized with OpenMP using 32 threads' even after leaving 12 hours there is no progress

Re: [gmx-users] g_hbond not running

Hi Toni, Have you tried with -nthreads 1, which effectively turns off the parallel grid search? Never seen/heard of this problem before. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory

Re: [gmx-users] g_hbond tool question

Dear Carlos, You get a double contribution from MainChain and SideChain in this way, don't you? Kind regards, Erik On 19 Nov 2014, at 03:00, Carlos Navarro Retamal cnava...@utalca.cl wrote: Dear gromacs users, I’m studying the hydrogen bond interaction between a protein and different

Re: [gmx-users] g_hbond

Hi, I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical

Re: [gmx-users] g_hbond

No. Strike that. The number of contacts is just reported the wrong way. It says Average number of contacts per timeframe 0.000… in the terminal but hbnum.xvg says different. Not sure if this applies to your problem. Erik Erik Marklund, PhD Postdoctoral Research Associate Department of

Re: [gmx-users] g_hbond

On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of

Re: [gmx-users] g_hbond

On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of

Re: [gmx-users] g_hbond

thank you very much, I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance . For my problem I would like to know all the atoms involved  (all the contacts) within of 4 Å. so I can understand which atoms can do salt bridge interactions.

[gmx-users] g_hbond

Hi all, I have created hydrogen bond existence map. In the index file generated using hbn option I can see following lines at the end: 1 2 1598 1 2 1851 1 2 1852 1 2 1862 10 11 1643 10 11 1651 10 11 1658 10

Re: [gmx-users] g_hbond

On 6/20/14, 6:23 AM, Nidhi Katyal wrote: Hi all, I have created hydrogen bond existence map. In the index file generated using hbn option I can see following lines at the end: 1 2 1598 1 2 1851 1 2 1852 1 2 1862 10 11 1643