[gmx-users] RMSF analysis
Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Thanks, Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSF analysis
What functional significance does it have, if any? --- According to my knowledge this reside is present in binding site.. and forms some hydrogen bonds with ligand What is the residue? -- *Glutamic Acid* What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? --* I measured Just C-alpha atoms.* Let me know On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/13 3:29 PM, Sainitin Donakonda wrote: Hi all, I recently performed MD simulation of protein - ligand complex..and analyzed its trajectory using RMSF tool in gromacs. This analysis revealed particular residue in binding site of protein showed quite high fluctuation around 0.30 nm but other residues were in range of 0.15 to 0.20 Can any body explain why this particular residue have high RMSF value in compared to other residues Doubtful, at least not without considerably more information. What functional significance does it have, if any? What is the residue? What did you measure - RMSF of the whole residue, just the backbone, just C-alpha, etc? Higher RMSF means the residue flops around more, i.e. your outcome indicates that the residue deviates from the average position to a greater extent than the other residues. Whether or not this actually means anything at all depends on your knowledge of the nature of the protein-ligand complex and the answers to the questions posed above. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue in ligand gyration analysis
Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyrate: munmap_chunk(): invalid pointer: 0x00b34140 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fdbb9e84b96] /usr/lib/libgmx.so.6(done_graph+0x35)[0x7fdbb96f25d5] /usr/lib/libgmx.so.6(gmx_rmpbc_done+0x36)[0x7fdbb96aa436] /usr/lib/libgmxana.so.6(gmx_gyrate+0xd0c)[0x7fdbba25000c] g_gyrate(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fdbb9e2776d] g_gyrate[0x400659] === Memory map: 0040-00401000 r-xp 08:02 939978 /usr/bin/g_gyrate 0060-00601000 r--p 08:02 939978 /usr/bin/g_gyrate 00601000-00602000 rw-p 1000 08:02 939978 /usr/bin/g_gyrate 00b05000-00c5f000 rw-p 00:00 0 [heap] 7fdbb7d56000-7fdbb7d6b000 r-xp 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7d6b000-7fdbb7f6a000 ---p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6a000-7fdbb7f6b000 r--p 00014000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6b000-7fdbb7f6c000 rw-p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6c000-7fdbb80b rw-p 00:00 0 7fdbb80b1000-7fdbb8153000 rw-p 00:00 0 7fdbb818c000-7fdbb8193000 rw-p 00:00 0 7fdbb81f4000-7fdbb85a3000 rw-p 00:00 0 7fdbb85a3000-7fdbb867c000 rw-p 00:00 0 7fdbb867c000-7fdbb8692000 r-xp 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8692000-7fdbb8891000 ---p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8891000-7fdbb8892000 r--p 00015000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8892000-7fdbb8893000 rw-p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8893000-7fdbb8895000 r-xp 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8895000-7fdbb8a95000 ---p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a95000-7fdbb8a96000 r--p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a96000-7fdbb8a97000 rw-p 3000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a97000-7fdbb8be8000 r-xp 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8be8000-7fdbb8de8000 ---p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8de8000-7fdbb8df r--p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df-7fdbb8df2000 rw-p 00159000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df2000-7fdbb8df3000 rw-p 00:00 0 7fdbb8df3000-7fdbb8f57000 r-xp 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb8f57000-7fdbb9156000 ---p 00164000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9156000-7fdbb9162000 r--p 00163000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9162000-7fdbb9163000 rw-p 0016f000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9163000-7fdbb925e000 r-xp 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb925e000-7fdbb945d000 ---p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945d000-7fdbb945e000 r--p 000fa000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945e000-7fdbb945f000 rw-p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945f000-7fdbb9477000 r-xp 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9477000-7fdbb9676000 ---p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9676000-7fdbb9677000 r--p 00017000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9677000-7fdbb9678000 rw-p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9678000-7fdbb967c000 rw-p 00:00 0 7fdbb967c000-7fdbb990a000 r-xp 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb990a000-7fdbb9b09000 ---p 0028e000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b09000-7fdbb9b0f000 r--p 0028d000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b0f000-7fdbb9b18000 rw-p 00293000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b18000-7fdbb9b19000 rw-p 00:00 0 7fdbb9b19000-7fdbb9c04000 r-xp 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9c04000-7fdbb9e04000 ---p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e04000-7fdbb9e05000 r--p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e05000-7fdbb9e06000 rw-p 000ec000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e06000-7fdbb9fbb000 r-xp 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbb9fbb000-7fdbba1ba000 ---p 001b5000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1ba000-7fdbba1be000 r--p 001b4000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1be000-7fdbba1c rw-p 001b8000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1c-7fdbba1c5000 rw-p 00:00 0 7fdbba1c5000-7fdbba349000 r-xp
Re: [gmx-users] Issue in ligand gyration analysis
Thank justin for reply i also thought same i used gromacs 4.5.5 here so just now i used gromacs 4.5.4 it works perfectly but choosing ligand only gives value as zero..can you tell me what might be the reason ? Thanks, Nitin On Fri, Aug 23, 2013 at 3:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/23/13 3:25 AM, Sainitin Donakonda wrote: Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyrate: munmap_chunk(): invalid pointer: 0x00b34140 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.**6(+0x7eb96)[0x7fdbb9e84b96] /usr/lib/libgmx.so.6(done_**graph+0x35)[0x7fdbb96f25d5] /usr/lib/libgmx.so.6(gmx_**rmpbc_done+0x36)[**0x7fdbb96aa436] /usr/lib/libgmxana.so.6(gmx_**gyrate+0xd0c)[0x7fdbba25000c] g_gyrate(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.**6(__libc_start_main+0xed)[** 0x7fdbb9e2776d] g_gyrate[0x400659] === Memory map: 0040-00401000 r-xp 08:02 939978 /usr/bin/g_gyrate 0060-00601000 r--p 08:02 939978 /usr/bin/g_gyrate 00601000-00602000 rw-p 1000 08:02 939978 /usr/bin/g_gyrate 00b05000-00c5f000 rw-p 00:00 0 [heap] 7fdbb7d56000-7fdbb7d6b000 r-xp 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_**s.so.1 7fdbb7d6b000-7fdbb7f6a000 ---p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_**s.so.1 7fdbb7f6a000-7fdbb7f6b000 r--p 00014000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_**s.so.1 7fdbb7f6b000-7fdbb7f6c000 rw-p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_**s.so.1 7fdbb7f6c000-7fdbb80b rw-p 00:00 0 7fdbb80b1000-7fdbb8153000 rw-p 00:00 0 7fdbb818c000-7fdbb8193000 rw-p 00:00 0 7fdbb81f4000-7fdbb85a3000 rw-p 00:00 0 7fdbb85a3000-7fdbb867c000 rw-p 00:00 0 7fdbb867c000-7fdbb8692000 r-xp 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.**1.2.3.4 7fdbb8692000-7fdbb8891000 ---p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.**1.2.3.4 7fdbb8891000-7fdbb8892000 r--p 00015000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.**1.2.3.4 7fdbb8892000-7fdbb8893000 rw-p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.**1.2.3.4 7fdbb8893000-7fdbb8895000 r-xp 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.**15.so http://libdl-2.15.so 7fdbb8895000-7fdbb8a95000 ---p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.**15.so http://libdl-2.15.so 7fdbb8a95000-7fdbb8a96000 r--p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.**15.so http://libdl-2.15.so 7fdbb8a96000-7fdbb8a97000 rw-p 3000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.**15.so http://libdl-2.15.so 7fdbb8a97000-7fdbb8be8000 r-xp 08:02 1048574 /usr/lib/x86_64-linux-gnu/**libxml2.so.2.7.8 7fdbb8be8000-7fdbb8de8000 ---p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/**libxml2.so.2.7.8 7fdbb8de8000-7fdbb8df r--p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/**libxml2.so.2.7.8 7fdbb8df-7fdbb8df2000 rw-p 00159000 08:02 1048574 /usr/lib/x86_64-linux-gnu/**libxml2.so.2.7.8 7fdbb8df2000-7fdbb8df3000 rw-p 00:00 0 7fdbb8df3000-7fdbb8f57000 r-xp 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb8f57000-7fdbb9156000 ---p 00164000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9156000-7fdbb9162000 r--p 00163000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9162000-7fdbb9163000 rw-p 0016f000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9163000-7fdbb925e000 r-xp 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.**15.so http://libm-2.15.so 7fdbb925e000-7fdbb945d000 ---p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.**15.so http://libm-2.15.so 7fdbb945d000-7fdbb945e000 r--p 000fa000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.**15.so http://libm-2.15.so 7fdbb945e000-7fdbb945f000 rw-p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.**15.so http://libm-2.15.so 7fdbb945f000-7fdbb9477000 r-xp 08:02 2354979 /lib/x86_64-linux-gnu/libpthre**ad-2.15.so http://libpthread-2.15.so 7fdbb9477000-7fdbb9676000 ---p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthre**ad-2.15.so http://libpthread-2.15.so 7fdbb9676000-7fdbb9677000 r--p 00017000 08:02 2354979 /lib/x86_64-linux-gnu/libpthre**ad-2.15.so http://libpthread-2.15.so 7fdbb9677000-7fdbb9678000 rw-p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthre**ad-2.15.so http://libpthread-2.15.so 7fdbb9678000-7fdbb967c000 rw-p 00:00 0 7fdbb967c000-7fdbb990a000 r-xp 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb990a000-7fdbb9b09000 ---p 0028e000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b09000-7fdbb9b0f000 r--p 0028d000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b0f000-7fdbb9b18000 rw-p 00293000 08:02 1046764
[gmx-users] Problem in Gyrate analysis
Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyrate: munmap_chunk(): invalid pointer: 0x00b34140 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fdbb9e84b96] /usr/lib/libgmx.so.6(done_graph+0x35)[0x7fdbb96f25d5] /usr/lib/libgmx.so.6(gmx_rmpbc_done+0x36)[0x7fdbb96aa436] /usr/lib/libgmxana.so.6(gmx_gyrate+0xd0c)[0x7fdbba25000c] g_gyrate(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fdbb9e2776d] g_gyrate[0x400659] === Memory map: 0040-00401000 r-xp 08:02 939978 /usr/bin/g_gyrate 0060-00601000 r--p 08:02 939978 /usr/bin/g_gyrate 00601000-00602000 rw-p 1000 08:02 939978 /usr/bin/g_gyrate 00b05000-00c5f000 rw-p 00:00 0 [heap] 7fdbb7d56000-7fdbb7d6b000 r-xp 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7d6b000-7fdbb7f6a000 ---p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6a000-7fdbb7f6b000 r--p 00014000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6b000-7fdbb7f6c000 rw-p 00015000 08:02 2354732 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fdbb7f6c000-7fdbb80b rw-p 00:00 0 7fdbb80b1000-7fdbb8153000 rw-p 00:00 0 7fdbb818c000-7fdbb8193000 rw-p 00:00 0 7fdbb81f4000-7fdbb85a3000 rw-p 00:00 0 7fdbb85a3000-7fdbb867c000 rw-p 00:00 0 7fdbb867c000-7fdbb8692000 r-xp 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8692000-7fdbb8891000 ---p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8891000-7fdbb8892000 r--p 00015000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8892000-7fdbb8893000 rw-p 00016000 08:02 2354831 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fdbb8893000-7fdbb8895000 r-xp 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8895000-7fdbb8a95000 ---p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a95000-7fdbb8a96000 r--p 2000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a96000-7fdbb8a97000 rw-p 3000 08:02 2354860 /lib/x86_64-linux-gnu/libdl-2.15.so 7fdbb8a97000-7fdbb8be8000 r-xp 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8be8000-7fdbb8de8000 ---p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8de8000-7fdbb8df r--p 00151000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df-7fdbb8df2000 rw-p 00159000 08:02 1048574 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fdbb8df2000-7fdbb8df3000 rw-p 00:00 0 7fdbb8df3000-7fdbb8f57000 r-xp 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb8f57000-7fdbb9156000 ---p 00164000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9156000-7fdbb9162000 r--p 00163000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9162000-7fdbb9163000 rw-p 0016f000 08:02 1053298 /usr/lib/libfftw3f.so.3.3.0 7fdbb9163000-7fdbb925e000 r-xp 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb925e000-7fdbb945d000 ---p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945d000-7fdbb945e000 r--p 000fa000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945e000-7fdbb945f000 rw-p 000fb000 08:02 2355059 /lib/x86_64-linux-gnu/libm-2.15.so 7fdbb945f000-7fdbb9477000 r-xp 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9477000-7fdbb9676000 ---p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9676000-7fdbb9677000 r--p 00017000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9677000-7fdbb9678000 rw-p 00018000 08:02 2354979 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fdbb9678000-7fdbb967c000 rw-p 00:00 0 7fdbb967c000-7fdbb990a000 r-xp 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb990a000-7fdbb9b09000 ---p 0028e000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b09000-7fdbb9b0f000 r--p 0028d000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b0f000-7fdbb9b18000 rw-p 00293000 08:02 1046764 /usr/lib/libgmx.so.6 7fdbb9b18000-7fdbb9b19000 rw-p 00:00 0 7fdbb9b19000-7fdbb9c04000 r-xp 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9c04000-7fdbb9e04000 ---p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e04000-7fdbb9e05000 r--p 000eb000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e05000-7fdbb9e06000 rw-p 000ec000 08:02 1049312 /usr/lib/libmd.so.6 7fdbb9e06000-7fdbb9fbb000 r-xp 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbb9fbb000-7fdbba1ba000 ---p 001b5000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1ba000-7fdbba1be000 r--p 001b4000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1be000-7fdbba1c rw-p 001b8000 08:02 2354975 /lib/x86_64-linux-gnu/libc-2.15.so 7fdbba1c-7fdbba1c5000 rw-p 00:00 0 7fdbba1c5000-7fdbba349000 r-xp
[gmx-users] Problem with PME in LIE
Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. and why we should use -rerun option beofre running LIE Regards, Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with PME in LIE
Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 8:54 AM, Sainitin Donakonda wrote: Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. The long-range mesh terms are not decomposable in a pairwise manner. LIE assumes that all of your interactions can be broken down from additive terms, and this is not the case with PME. and why we should use -rerun option beofre running LIE If you evaluate the energies from a PME simulation, the result will be off. If you use plain cutoffs for the dynamics, the simulation will probably be junk. So one solution is to run the simulation with PME to get reasonable dynamics, then post-process via mdrun -rerun while evaluating energies with plain cutoffs (which one would usually increase beyond normal values, IIRC, but I do not use LIE myself). -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with PME in LIE
Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 9:21 AM, Sainitin Donakonda wrote: Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Which simulation stage do you normally use to collect data? -Justin Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 8:54 AM, Sainitin Donakonda wrote: Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. The long-range mesh terms are not decomposable in a pairwise manner. LIE assumes that all of your interactions can be broken down from additive terms, and this is not the case with PME. and why we should use -rerun option beofre running LIE If you evaluate the energies from a PME simulation, the result will be off. If you use plain cutoffs for the dynamics, the simulation will probably be junk. So one solution is to run the simulation with PME to get reasonable dynamics, then post-process via mdrun -rerun while evaluating energies with plain cutoffs (which one would usually increase beyond normal values, IIRC, but I do not use LIE myself). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with PME in LIE
Ok..thanks...so i will use -rerun option in final production ..step..as follows...actually i ran 20 ns MD simulation so i used extend option to run everything in cluster in correct time #first 10 ns grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_10.tpr mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10 #extension for 10 more ns tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi MD_first10.cpt -np 32 Can you please tell is this commands are appropriate for production run using -rerun option...in help manual it is mentioned that Neighbor searching will be performed for every frame, unless nstlist is zero.. should i set nslist to zero in MDP file? Thanks On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 10:12 AM, Sainitin Donakonda wrote: Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. And there you have it. LIE is just an analysis method like anything else. There is no purpose in my mind in reanalyzing nonbonded energies during equilibration. -Justin thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 9:21 AM, Sainitin Donakonda wrote: Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Which simulation stage do you normally use to collect data? -Justin Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 8:54 AM, Sainitin Donakonda wrote: Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. The long-range mesh terms are not decomposable in a pairwise manner. LIE assumes that all of your interactions can be broken down from additive terms, and this is not the case with PME. and why we should use -rerun option beofre running LIE If you evaluate the energies from a PME simulation, the result will be off. If you use plain cutoffs for the dynamics, the simulation will probably be junk. So one solution is to run the simulation with PME to get reasonable dynamics, then post-process via mdrun -rerun while evaluating energies with plain cutoffs (which one would usually increase beyond normal values, IIRC, but I do not use LIE myself). -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/**listinfo/gmx-users h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search**h**ttp://www.gromacs.org/**Support/**http://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://**www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/**Support/**Mailing_Listshttp://www.gromacs.org/Support/**Mailing_Lists http:/**/www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department
Re: [gmx-users] Problem with PME in LIE
I started MD very recently dont have much experience you said i would need .tpr file which doesnot use PME ? how can i get that ? Thanks, Nitin On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 10:43 AM, Sainitin Donakonda wrote: Ok..thanks...so i will use -rerun option in final production ..step..as follows...actually i ran 20 ns MD simulation so i used extend option to run everything in cluster in correct time #first 10 ns grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_10.tpr mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10 #extension for 10 more ns tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi MD_first10.cpt -np 32 Can you please tell is this commands are appropriate for production run using -rerun option...in help manual it is mentioned that Neighbor You will need a new .tpr file that does not use PME. Then, I would suggest concatenating the existing .xtc files to streamline the process. I also do not recall whether the -rerun option works in parallel, but in any case it is reasonably fast even in serial. Thus: mdrun -s newtpr.tpr -rerun full20ns.xtc searching will be performed for every frame, unless nstlist is zero.. should i set nslist to zero in MDP file? No. You want the neighbor list to be updated at every frame in the .xtc, otherwise you will miss interactions and the output will likely be flawed. -Justin Thanks On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 10:12 AM, Sainitin Donakonda wrote: Usually i collect data after final production run...after this i take .xtc file and analyze it using various gromacs tools .. And there you have it. LIE is just an analysis method like anything else. There is no purpose in my mind in reanalyzing nonbonded energies during equilibration. -Justin thanks, nitin On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 9:21 AM, Sainitin Donakonda wrote: Hi justin, Thanks for explaination .. i already ran MD for both ligand alone and protein ligand complex.. So now can you please tell me where should use mdrun -rerun option ..i mean at which stage ..should i used in Energy miniminimzation or NVT and NPT equilibration or Production run .. Or should i use mdrun -rerun option at every stage ...? or it should be used only at final production run? Which simulation stage do you normally use to collect data? -Justin Thanks, Nitin On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/17/13 8:54 AM, Sainitin Donakonda wrote: Hi , I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. The long-range mesh terms are not decomposable in a pairwise manner. LIE assumes that all of your interactions can be broken down from additive terms, and this is not the case with PME. and why we should use -rerun option beofre running LIE If you evaluate the energies from a PME simulation, the result will be off. If you use plain cutoffs for the dynamics, the simulation will probably be junk. So one solution is to run the simulation with PME to get reasonable dynamics, then post-process via mdrun -rerun while evaluating energies with plain cutoffs (which one would usually increase beyond normal values, IIRC, but I do not use LIE myself). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalemkul@outerbanks.**umaryla**nd.eduhttp://umaryland.edu jalemkul@outerbanks.**umaryland.edujalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users ht**tp://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users htt**p://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users h**ttp://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org
[gmx-users] Problem with energy minimization parameters
Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is failed in Energy minimization step itself.. showing following error *Error : whole protein drug complex * * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated * Then i looked up http://www.gromacs.org/Documentation/Terminology/Blowing_Up In this i followed up suggestions which are mentioned in diagnosing unstable system as follows. First i did energy minimization for protein alone which worked perfectly with out any error. Second i did energy minimization for ligand alone (with out protein)..this showed again following error.. Error 2 : Ligand only Fatal error: *184 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.* So there is problem with small molecule...not with the protein ..here i think i should tune parameters in .MDP file..which i m just not getting how to do.. here is the EM.mdp file.. ; LINES STARTING WITH ';' ARE COMMENTS title= Minimization; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.01 ; 7.3.9 Neighbor Searching nstlist = 1; [steps] freq to update neighbor list nstxout = 1 ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Can any body please tell me how to optimize these parameters Thanks, Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Problem with energy minimization parameters
Hi Justin, Thanks for suggestion...and pointing out that there is problem with topology ...now i checked ligand file..there hydrogens were not added correctly..so swissparam tool was not correct topology .. now i corrected it ..it works perfectly .. Thanks a lot Sainitin On Tue, Jul 16, 2013 at 5:05 PM, Sainitin Donakonda saigr...@gmail.comwrote: Hi all, I have 3 protein-drug complexes (same protein and different drugs) i performed 20 ns molecular dynamics simulation..using same parameters (i mean energy minimzation parameters) ..2 of them was successful for MD simulation..(im using Charmm 27 Force field) But 1 drug protein complex is failed in Energy minimization step itself.. showing following error *Error : whole protein drug complex * * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated * Then i looked up http://www.gromacs.org/Documentation/Terminology/Blowing_Up In this i followed up suggestions which are mentioned in diagnosing unstable system as follows. First i did energy minimization for protein alone which worked perfectly with out any error. Second i did energy minimization for ligand alone (with out protein)..this showed again following error.. Error 2 : Ligand only Fatal error: *184 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.* So there is problem with small molecule...not with the protein ..here i think i should tune parameters in .MDP file..which i m just not getting how to do.. here is the EM.mdp file.. ; LINES STARTING WITH ';' ARE COMMENTS title= Minimization; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.01 ; 7.3.9 Neighbor Searching nstlist = 1; [steps] freq to update neighbor list nstxout = 1 ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Can any body please tell me how to optimize these parameters Thanks, Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue with g_lie
Hi Everybody, I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE and what is the isssue with PME .. Regards, Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue with RMSD for protein drug complex
Hi all, I ran 20ns simulation on protein drug complex..now i want to check overall stability of this complex to acheive this i did following i supplied index file and choose Protein_Lig option for both least square fit and RMSD calculation..i used following command g_rms -f em.tpr (intital structure before production run) -s file.xtc (with out pbc) -n index.ndx -o complex.xvg is this correct way to determine overall stability of the complex ? or should i use only back bone of protein? Can any body let me know about it ? Thanks in Advance Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Visualize Protein ligand complex
Hi Tsjerk, Thanks for information i limited number of frames ..which worked perfectly :) Cheers, Sainitin On Thu, Jun 27, 2013 at 8:06 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sainitin, You can extract only the protein and ligand, using a suitable index file, or you can limit the number of frames. Cheers, Tsjerk On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger kronenberg...@gmail.com wrote: Don't you wanna try to use the VMD use vmd xxx.gro yyy.trr and then you could highlight your ligand 2013/6/27 Sainitin Donakonda saigr...@gmail.com Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize complex Can anybody tell me command how to visualize protein ligand complex trajectory in pymol Thanks, Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue with RMSD for protein drug complex
Hi Justin, Thank your very much for reply i have done both ways i also have backbone RMSD data so i will consider only this in my analysis. Cheers, Sainitin On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/4/13 5:17 AM, Sainitin Donakonda wrote: Hi all, I ran 20ns simulation on protein drug complex..now i want to check overall stability of this complex to acheive this i did following i supplied index file and choose Protein_Lig option for both least square fit and RMSD calculation..i used following command g_rms -f em.tpr (intital structure before production run) -s file.xtc (with out pbc) -n index.ndx -o complex.xvg is this correct way to determine overall stability of the complex ? or should i use only back bone of protein? Using the whole complex probably obscures detail. Using the backbone or Calpha atoms is much more common, because it gives you some insight into the changes within the fold of the protein. I guess it all depends on how you define stability and what you want to measure, but if you're trying to assess the stability of the protein's structure, I wouldn't measure it like you're doing. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue in Energy minimization protein-ligand complex
Hi all, I have set of 5 different drugs which are complexed with same protein (homology model). So i wanted to run MD simulation using gromacs. I followed one procedure as follows 1) I took homology model and minimized it 2) Then followed general procedure of simulation in gromacs. 4 drugs with same protein simulation was successful. Unfortunately 1 drug among these 5 drugs showing error at energy minimization step although i used same em.mdp file which is used in other four simulations.. *Error :* * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated* * * This means system blowing up at energy minimization step itself ..just I dont know whats the problem.. Can anybody tell me how to solve this issue..major problem here is same energy minimization step using .mdp file as mentioned above .dont know why this is failing for this particular protein-drug complex. em.mdp which i used in in all 5 simulations as follows ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = Protein LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.002 ; 7.3.9 Neighbor Searching nstlist = 5; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Thanks, sainitin Thanks, Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue in Energy minimization protein-ligand complex
Hi Justin, Thanks for reply. using pdbgmx i generated charmm27 force field for protein I prepared ligand topologies using swissparam online tool for all 5 ligands. But it worked for 4 and 5th one is creating problem at energy minimization step. Thanks -sainitin On Thu, Jul 4, 2013 at 9:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/4/13 3:00 PM, Sainitin Donakonda wrote: Hi all, I have set of 5 different drugs which are complexed with same protein (homology model). So i wanted to run MD simulation using gromacs. I followed one procedure as follows 1) I took homology model and minimized it 2) Then followed general procedure of simulation in gromacs. 4 drugs with same protein simulation was successful. Unfortunately 1 drug among these 5 drugs showing error at energy minimization step although i used same em.mdp file which is used in other four simulations.. *Error :* * * *708 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.* *This usually means that your system is not well equilibrated* * * This means system blowing up at energy minimization step itself ..just I dont know whats the problem.. Can anybody tell me how to solve this issue..major problem here is same energy minimization step using .mdp file as mentioned above .dont know why this is failing for this particular protein-drug complex. How did you prepare the initial configurations? How did you create the ligand topology? One or the other is your problem. -Justin em.mdp which i used in in all 5 simulations as follows ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run define = -DFLEX_TI3P; defines to pass to the preprocessor constraints = none ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate energygrps = Protein LIG; group(s) to write to energy file ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size dt = 0.002 ; 7.3.9 Neighbor Searching nstlist = 5; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; [nm] Cut-off distance from the long-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.2 ; Start switching th LJ potential DispCorr= Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb optimize_fft= yes Thanks, sainitin Thanks, Sainitin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting
[gmx-users] Visualize Protein ligand complex
Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize complex Can anybody tell me command how to visualize protein ligand complex trajectory in pymol Thanks, Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem in RMSD plot
Hi, Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2 parts first i ran 10ns and extended to another 10ns.. Then I got 2 .xtc files...i combined both these trajectories using following command trjcat -f 1.xtc 2.xtc -o combine.xtc -cat Then using combine.xtc i plotted RMSD plot for protein back bone i got the plot but it is strange there is a line from 0 ns passing as daignol Here i attach that plot.. Can any body suggest how to solve this issue.. Thanks, Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Increasing performance of siumulation in cluster
Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Increasing performance of siumulation in cluster
Hi Mark, I forgot to mention about simulation it is protein ligand simulation which contains one protein and ligand with 2 solute molecules..and regarding hardware of cluster which is in my university as follows CPUs AMD Opteron 6274 number of cores 5888 th. peak performance 51.8 TFlops compute nodes 4-way nodes *Saxonid* with 64 cores nodes with 64 GB RAM 48 nodes with 128 GB RAM 24 nodes with 256 GB RAM 12 nodes with 512 GB RAM 8 Can you now suggest some methods which i can use to optimize to increase performance Thanks, Nitin On Fri, May 31, 2013 at 10:54 AM, Mark Abraham mark.j.abra...@gmail.comwrote: There are lots of things you might do, but when we don't know what's in the simulation or anything about the hardware, nobody can tell. Mark On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda saigr...@gmail.com wrote: Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Increasing performance of siumulation in cluster
Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue running gromacs in Cluster
Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; maximum number of steps to integrate ; 7.3.8 Output Control nstxout = 200 ; suppress .trr output nstvout = 200; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.8 ; Start switching th LJ potential DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = V-rescale ; temperature coupling with Berendsen-thermostat tc_grps = Protein_LIG Water_and_ions; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain *and im using following commands dividing 20 ns to 10 ns each via extending simulation* *#This is the first simulation MD.mdp file contains 20 ns setup* grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 *#This extends 10 ns simulation* tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 But it is crashed giving following error *XTC error - maybe you are out of quota?* * * *dont know why it happened it is because as im saving .trr file every 200ps? is it creating large files? or should i give different name in extending simulation?* * * *Please help* * * *Thanks,* *Nitin* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Issue running gromacs in Cluster
Thank you very much for inputs but i forgot to mention in previous query i got one error ..with other protein ligand simulation i used same MD file saving 200 steps.. *Cannot write trajectory frame; maybe you are out of quota?* * * Whats the solution for this error ? is this same problem with saving 200 steps? or some thing else Thanks, Sainitin On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard richard.broadben...@imperial.ac.uk wrote: On 13/05/2013 08:46, Sainitin Donakonda saigr...@gmail.com wrote: Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500; maximum number of steps to integrate ; 7.3.8 Output Control nstxout = 200 ; suppress .trr output nstvout = 200; suppress .trr output This writes out every 0.4 ps I doubt that¹s what you want nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = Protein LIG ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off rvdw_switch = 0.8 ; Start switching th LJ potential DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = V-rescale ; temperature coupling with Berendsen-thermostat tc_grps = Protein_LIG Water_and_ions; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling= com ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation= yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain *and im using following commands dividing 20 ns to 10 ns each via extending simulation* *#This is the first simulation MD.mdp file contains 20 ns setup* grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 *#This extends 10 ns simulation* tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 But it is crashed giving following error *XTC error - maybe you are out of quota?* * * *dont know why it happened it is because as im saving .trr file every 200ps? is it creating large files? or should i give different name in extending simulation?* No you are writing every 200 steps not ps this is explained in the turtorials and the manual You can check the file size by looking at ls -lh my guess is both the trr and xtc will be gigantic
[gmx-users] Problem with DSSP
Hello, I am trying to secondary structure analysis using DSSP in gromacs so i followed this procedure First I downloaded dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O ~/dssp this gave dssp executable file in my home directory I checked ./dssp ...it works Then i set environment variable as follows export DSSP=/myhomedir/dssp/dssp then i executed following command in gromacs do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10 But this gives following error *Program do_dssp, VERSION 4.5.4 Source code file: /home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516 Fatal error: DSSP executable (/home/dssp) does not exist (use setenv DSSP)* * * *Can any body explain where it went wrong...* *I have gone through gromacs list but unfortunately couldnot manage to solve this simple issue* * * *Thanks,* *Nitin* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Issue with RMSD profile
Hello all, I ran 10ns molecular dynamics simulation of protein ligand complex ..in which protein homology model..finally i analyzed .xtc file which is produced after MD production run..first i plotted RMSD profile of backbone of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it is stabilized in plateau.. My question is fluctuation in RMSD profile from 0.2nm to 0.4 nm is acceptable range or not? Can any body explain this Thank you very much Cheers, Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with gromacs in Cluster
Hey all, I recently ran 20ns simulation of protein ligand complex on cluster i used following script to run simulation grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_test.tpr mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 *I saved this as MD.sh And then submited to cluster using following script* #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 8,8 # number of processors Min,Max #BSUB -o test/output_%J.log # output file #BSUB -e test/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd test echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` It gave result but when checked files .xtc and created RMSD plots in that x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns.. Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF run time limit. Exited with exit code 140. i gave maximum cluster time 120 hours..still it is not sufficient .. Can any body tell me how do it split script i such that i will get all 20ns simulation Thanks in advance , Sainitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
