Hi Mark,
Thanks for your quick response.
In the all three minimisation.mdp files (the one for water.pdb,
substrate.pdb and merged.pdb) I have:
pbc = xyz
To minimise the water.pdb file I have:
periodic_molecules = no ;
To minimise the substrate.pdb and then the merged.pdb I have:
periodic_molecules = yes ;
Is this what you meant?
When I minimise substrate.pdb or water.pdb alone it works. When I combine
them and minimise merged.pdb it doesn¹t.
Cheers,
Amanda
>--
>
>Message: 5
>Date: Sun, 26 Jun 2016 09:53:46 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se"
> <gromacs.org_gmx-users@maillist.sys.kth.se>
>Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate
>Message-ID:
> <camnumat12f5adcfp8rq3cvft21vyveqkbdt0lykrnwwlgrg...@mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>You're presumably making one of your formerly periodic dimensions
>differently periodic when you combine your boxes. If your input structure
>has molecules with coordinates that are broken across the former boundary,
>you need to make them whole before your merge can work sanely.
>
>Mark
>
>On Sun, Jun 26, 2016 at 11:45 AM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Dear Gromacs users,
>>
>> I am want to simulate water on a substrate.
>> I have a water.pdb file with the coordinates of a cuboid of water and a
>> substrate.pdb file with the coordinates of the substrate. The box
>> dimensions along the x and y directions are identical for both files.
>> I run two simulations to minimise both structures separately. I get no
>> error, meaning the topology file must be correct (is this a correct
>> assumption?) This also ensures that all atoms in the minimised.pdb files
>> are within the box I have specified (as opposed to before, when some
>>atoms
>> were slightly outside).
>> I then have a script to merge both minimised .pdb files.
>> I minimise the system and get a segmentation fault:
>>
>> 40783 Segmentation fault
>>
>> Further, in the file.log I get:
>>
>>
>> Steepest Descents:
>>
>>Tolerance (Fmax) = 6.0e+01
>>
>>Number of steps= 10
>>
>>Step Time Lambda
>>
>> 00.00.0
>>
>>
>>Energies (kJ/mol)
>>
>>Bond Angle LJ-14 Coulomb-14LJ
>>(SR)
>>
>> 1.36501e+046.58753e+044.22206e+04 -1.70332e+06
>>-nan
>>
>>Coulomb (SR) Coul. recip. Potential Pressure (bar)
>>
>> 1.18196e+062.65781e+03 -nan -nan
>>
>>
>>
>> I have visualised the input merged.pdb file and have also checked the
>> minimum and maximum coordinates of water and substrate and I am sure
>>there
>> is no atom overlap. In fact, water and substrate atoms are separate by
>>more
>> than 3A. ( I have also tried previously with smaller separations).
>>
>> What could else could I check?
>>
>> Thanks,
>> Amanda
>> --
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>
>
>--
>
>Message: 6
>Date: Sun, 26 Jun 2016 09:53:46 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se"
> <gromacs.org_gmx-users@maillist.sys.kth.se>
>Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate
>Message-ID:
> <camnumat12f5adcfp8rq3cvft21vyveqkbdt0lykrnwwlgrg...@mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi,
>
>You're presumably making one of your formerly periodic dimensions
>differently periodic when you combine your boxes. If your input structure
>has molecules with coordinates that are broken across the former boundary,
>you need to make them whole before your merge can work sanely.
>
>Mark
>
>On Sun, Jun 26, 2016 at 11:45 AM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Dear Gromacs users,
>>
>>
