[gmx-users] FW: Re: Re: liquid-solid/liquid-air interface simulations
Dear gmx users, I ran across this 2016 response mentioning titania. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/105969 .html I am familiar with Gromacs using it to model protein adsorption onto polymers. Now I need to look at a film drying on TiO2. What I have done to date for the air liquid is to create a tall box and use editconf to layer ,say an acrylate in alcohol , in the bottom region near a polymer surface and N2 ( as air ) in the top of the box. Results "look " reasonable in that the organic generally adsorbs and the alcohol and N2 mix. But this does not approach evaporation, ( alcohol dissipates, N2 hangs around ) Do I need to make a very larger box ?? For polymer surfaces I modify the n2t file to add any atom types not included in oplsaa or 45a7 ff and then follow with x2top . But I've not gotten very far with this method with oxides. This is where I could use a few pointers. Any hints some bullet points on creating an oxide surface and perhaps faults to avoid in mimicking an air liquid interface would be appreciated, Regards, Paul Paul Buscemi, Ph.D. UMN BICB -- 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.
[gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)
Dear All, I am going through very bad phase while analyzing huge trajectories (23 GB, POPC membrane protein systems: Atoms: 201382) using HPC system installed at HPC facility of Denmark Technical University, Denmark. I have checked the trajectory, which seems fine with the gmx check command... Though it reads the trajectories but while writing the compressed forms after reading all the frames, it shows the following error.. *** Error in `gmx': munmap_chunk(): invalid pointer: 0x7f76c609386e *** === Backtrace: = /lib64/libc.so.6(+0x7f574)[0x7f76c3fa6574] /appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_Z8done_topP10t_topology+0x39)[0x7f76c5263f59] /appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(gmx_trjconv+0x1a3a)[0x7f76c54e6ffa] /appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x261)[0x7f76c5143ca1] gmx[0x40e58c] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f76c3f493d5] gmx[0x40e651] === Memory map: 0040-0043f000 r-xp 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx 0063e000-0063f000 r--p 0003e000 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx 0063f000-0064 rw-p 0003f000 00:bb 70350544 /appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx 01506000-01d83000 rw-p 00:00 0 [heap] 7f76c1ca5000-7f76c1ce3000 r-xp 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0 7f76c1ce3000-7f76c1ee3000 ---p 0003e000 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0 7f76c1ee3000-7f76c1ee4000 rw-p 0003e000 00:bb 64559031 /appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0 7f76c1ee4000-7f76c2003000 r-xp 08:05 518663 /usr/lib64/libgfortran.so.3.0.0 7f76c2003000-7f76c2203000 ---p 0011f000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0 7f76c2203000-7f76c2204000 r--p 0011f000 08:05 518663 /usr/lib64/libgfortran.so.3.0.0 7f76c2204000-7f76c2206000 rw-p 0012 08:05 518663 /usr/lib64/libgfortran.so.3.0.0 7f76c2206000-7f76c220f000 r-xp 08:05 516182 /usr/lib64/libltdl.so.7.3.0 7f76c220f000-7f76c240e000 ---p 9000 08:05 516182 /usr/lib64/libltdl.so.7.3.0 7f76c240e000-7f76c240f000 r--p 8000 08:05 516182 /usr/lib64/libltdl.so.7.3.0 7f76c240f000-7f76c241 rw-p 9000 08:05 516182 /usr/lib64/libltdl.so.7.3.0 7f76c241-7f76c241a000 r-xp 08:05 515617 /usr/lib64/libnuma.so.1 7f76c241a000-7f76c261a000 ---p a000 08:05 515617 /usr/lib64/libnuma.so.1 7f76c261a000-7f76c261b000 r--p a000 08:05 515617 /usr/lib64/libnuma.so.1 7f76c261b000-7f76c261c000 rw-p b000 08:05 515617 /usr/lib64/libnuma.so.1 7f76c261c000-7f76c31c5000 r-xp 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so 7f76c31c5000-7f76c33c5000 ---p 00ba9000 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so 7f76c33c5000-7f76c33d3000 rw-p 00ba9000 00:bb 31025797 /appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so 7f76c33d3000-7f76c34e2000 rw-p 00:00 0 7f76c34e2000-7f76c36d r-xp 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8 7f76c36d-7f76c38cf000 ---p 001ee000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8 7f76c38cf000-7f76c38e r--p 001ed000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8 7f76c38e-7f76c38e1000 rw-p 001fe000 00:bb 70339951 /appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8 7f76c38e1000-7f76c38e8000 r-xp 08:05 515140 /usr/lib64/librt-2.17.so 7f76c38e8000-7f76c3ae7000 ---p 7000 08:05 515140 /usr/lib64/librt-2.17.so 7f76c3ae7000-7f76c3ae8000 r--p 6000 08:05 515140 /usr/lib64/librt-2.17.so 7f76c3ae8000-7f76c3ae9000 rw-p 7000 08:05 515140 /usr/lib64/librt-2.17.so 7f76c3ae9000-7f76c3aeb000 r-xp 08:05 515116 /usr/lib64/libdl-2.17.so 7f76c3aeb000-7f76c3ceb000 ---p 2000 08:05 515116 /usr/lib64/libdl-2.17.so 7f76c3ceb000-7f76c3cec000 r--p 2000 08:05 515116 /usr/lib64/libdl-2.17.so 7f76c3cec000-7f76c3ced000 rw-p 3000 08:05 515116 /usr/lib64/libdl-2.17.so 7f76c3ced000-7f76c3d26000 r-xp 08:05 516184 /usr/lib64/libhwloc.so.5.6.8 7f76c3d26000-7f76c3f25000 ---p
Re: [gmx-users] Lateral pressure
Thanks for your answers ... But what I need is the pressure as a function of z ... not as a function of time... So I think the only thing I have to do is to use Gromacs - LS as suggested by Kevin ? Best regards Candy Le sam. 22 sept. 2018 à 00:27, Alex a écrit : > gmx energy lets you plot the components of the pressure tensor, the Z-Z > term is one of them. > > Alex > > > On 9/21/2018 2:52 AM, Candy Deck wrote: > > Dear Gromacs Users, > > > > Is there a way to get the lateral pressure with Gromacs ? > > I am willing to get the variation of pressure along z. > > > > Thanks ! > > -- > 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.
[gmx-users] GMX Helix Segmentation fault
Dear All, Hello. I am doing analysis soem analysis of TM helix properties using the GMX helix tool of GROMACS 2018.2. Though, in someways its working in the old version 2016.2 but its not working in the latest 2018.2 version. I have appended the following error. gmx helix -f ../md.xtc -s ../md.tpr -n index.ndx Reading file ../md.tpr, VERSION 2018.2 (single precision) Reading frame 0 time 20.000 Please select a group containing the entire backbone Group 0 ( System) has 201382 elements Group 1 (Protein) has 22327 elements Group 2 ( Protein-H) has 11159 elements Group 3 (C-alpha) has 1414 elements Group 4 ( Backbone) has 4242 elements Group 5 ( MainChain) has 5651 elements Group 6 ( MainChain+Cb) has 6978 elements Group 7 (MainChain+H) has 6986 elements Group 8 ( SideChain) has 15341 elements Group 9 (SideChain-H) has 5508 elements Group10 (Prot-Masses) has 22327 elements Group11 (non-Protein) has 179055 elements Group12 ( Other) has 179055 elements Group13 ( POPC) has 40468 elements Group14 ( TIP3) has 138315 elements Group15 (SOD) has 146 elements Group16 (CLA) has 126 elements Group17 ( a_10743-11091) has 349 elements Select a group: 17 Selected 17: 'a_10743-11091' Checking group a_10743-11091 There are 21 residues There are 19 complete backbone residues (from 2 to 20) nall=349 Reading file ../md.tpr, VERSION 2018.2 (single precision) Please help me to rectify this error or suggest any idea how should I get reed of this. Thanking you With Warm Regards Budheswar -- 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.
