[gmx-users] GMX hbond

[Justin Lemkul]

On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:
> I tried, didn't find the proper answer. I run the simulation using Gromacs 4.5 version and used g_hbond successfully.  Could not find out why its not working using gmx hbond.

No version of GROMACS should have ever worked with such index groups.

A hydrogen bond must be defined by at least three atoms, because it is 
based on both the D-A distance and the D-H-A angle. One cannot do the 
analysis on a group that contains only H atoms. Your donors have to 
include both D and H atoms, and the acceptor group the A atoms.

-Justin

> Nilesh
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Tuesday, April 10, 2018 6:39:37 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GMX hbond
>
>
>
> On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
>> Hello Gromacs users,
>>
>>
>> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION 5.1.4. I did following steps
>>
>> mx hbond -f traj.trr -s md.tpr -n index.ndx -ac
>>
>> Reading file md.tpr, VERSION 5.1.4 (single precision)
>> Specify 2 groups to analyze:
>> Group     0 (         System) has  2560 elements
>> Group     1 (          Other) has  2432 elements
>> Group     2 (            EMI) has  2432 elements
>> Group     3 (             CL) has   128 elements
>> Group     4 (            Ion) has   128 elements
>> Group     5 (            EMI) has  2432 elements
>> Group     6 (             CL) has   128 elements
>> Group     7 (              C) has   128 elements
>> Group     8 (             C2) has   128 elements
>> Group     9 (             C4) has   128 elements
>> Group    10 (             H9) has   128 elements
>> Group    11 (            H10) has   128 elements
>> Group    12 (            H11) has   128 elements
>> Group    13 (             CL) has   128 elements
>> Group    14 (             ch) has   256 elements
>> Group    15 (             ch) has     3 elements
>> Group    16 (             O1) has     2 elements
>> Select a group: 14
>> Selected 14: 'ch'
>> Select a group: 13
>> Selected 13: 'CL'
>> Checking for overlap in atoms between ch and CL
>> Calculating hydrogen bonds between ch (256 atoms) and CL (128 atoms)
>> Found 0 donors and 0 acceptors
>> Making hbmap structure...done.
>> No Donors or Acceptors found
>>
>> -------------------------------------------------------
>> Program gmx hbond, VERSION 5.1.4
>> Source code file: /home/software/gromacs-5.1.4/src/gromacs/gmxana/gmx_hbond.c, l                                                                                                              ine: 3984
>>
>> Fatal error:
>> Nothing to be done
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Group 14 is list of donor hydrogen (eg. 4(donor)     11(hydrogen)) and group is list of acceptors . Why donors and acceptors are zero.
> Have you tried Googling the error? The first result has the answer...
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================