[gmx-users] g_hbond problems

[Justin Lemkul]

On 3/10/17 4:51 AM, andrea.correa at 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 a segmentation fault with the message:
>
>> Select a group: 6
>> Selected 6: 'PEI_&_OC'
>> Select a group: 3
>> Selected 3: 'Water'
>> Checking for overlap in atoms between PEI_&_OC and Water
>> Calculating hydrogen bonds between PEI_&_OC (1296 atoms) and Water (258 atoms)
>> Found 86 donors and 1382 acceptors
>> Reading frame       0 time 10000.000   Will do grid-seach on 15x15x15 grid,
>> rcut=0.35
>> Segmentation fault (core dumped)
>
> The number of donors is correct (I have 86 water molecules) but the number of
> acceptors is not.
>

The number of acceptors is correct.  Water oxygens can be acceptors, so 1296 + 
86 = 1382.

> Please, can someone tell me what I am doing wrong?

What GROMACS version are you using?

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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