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 +0000 >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) = 6.00000e+01 >> >> Number of steps = 100000 >> >> Step Time Lambda >> >> 0 0.00000 0.00000 >> >> >> Energies (kJ/mol) >> >> Bond Angle LJ-14 Coulomb-14 LJ >>(SR) >> >> 1.36501e+04 6.58753e+04 4.22206e+04 -1.70332e+06 >>-nan >> >> Coulomb (SR) Coul. recip. Potential Pressure (bar) >> >> 1.18196e+06 2.65781e+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 >> -- >> 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-requ...@gromacs.org. >> > > >------------------------------ > >Message: 6 >Date: Sun, 26 Jun 2016 09:53:46 +0000 >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) = 6.00000e+01 >> >> Number of steps = 100000 >> >> Step Time Lambda >> >> 0 0.00000 0.00000 >> >> >> Energies (kJ/mol) >> >> Bond Angle LJ-14 Coulomb-14 LJ >>(SR) >> >> 1.36501e+04 6.58753e+04 4.22206e+04 -1.70332e+06 >>-nan >> >> Coulomb (SR) Coul. recip. Potential Pressure (bar) >> >> 1.18196e+06 2.65781e+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 >> -- >> 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-requ...@gromacs.org. >> > > >------------------------------ > >-- >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-requ...@gromacs.org. > >End of gromacs.org_gmx-users Digest, Vol 146, Issue 142 >******************************************************* -- 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-requ...@gromacs.org.