Re: [gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5
On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham wrote: > Hi, > > That shouldn't happen if your MPI library is working (have you tested it > with other programs?) and configured properly. It's possible this is a > known bug, so please let us know if you can reproduce it in the latest > releases. > > Mark > > > Hi, I installed different versions of gromacs with the same MPI library. Surprisingly, the problem doesn't occur in gromacs-4.5.1.. but still in the gromacs-4.6.3... The MPI version is MVAPICH2-1.9a for infinite band. Best, Qin On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao wrote: > > > Dear all, > > > > I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT > > ensemble, and I got the following errors when I tried to use 2 cores per > > replica: > > > > "[node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: > Segmentation > > fault (signal 11) > > [node-ib-13.local:mpi_rank_63][error_sighandler] Caught error: > Segmentation > > fault (signal 11) > > ... > > " > > > > Surprisingly, it worked fine when I tried to use only 1 core per > replica.. > > I have no idea what caused the problem.. Could you give me some advice? > > > > ps. the command I used is > > "srun .../gromacs-4.5.5-mpi-slurm/bin/mdrun_infiniband -s remd_.tpr > -multi > > 48 -replex 1000 -deffnm remd_ -cpi remd_.cpt -append" > > > > Best > > Qin > > -- > > 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] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5
Dear all, I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT ensemble, and I got the following errors when I tried to use 2 cores per replica: "[node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: Segmentation fault (signal 11) [node-ib-13.local:mpi_rank_63][error_sighandler] Caught error: Segmentation fault (signal 11) ... " Surprisingly, it worked fine when I tried to use only 1 core per replica.. I have no idea what caused the problem.. Could you give me some advice? ps. the command I used is "srun .../gromacs-4.5.5-mpi-slurm/bin/mdrun_infiniband -s remd_.tpr -multi 48 -replex 1000 -deffnm remd_ -cpi remd_.cpt -append" Best Qin -- 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] Error in Installing gromacs4.6.3 with mpi
On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham wrote: > No idea if it's causing your problem, but you need all the Ds in > -DBUILD_SHARED_LIBS=no > > Mark > > On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao wrote: > > Dear all, > > > > I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster > > and got the following error in step 'make': > > > > "/usr/bin/ld: > > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation > > R_X86_64_32 against `.bss' can not be used when making a shared object; > > recompile with -fPIC > > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad > > value > > " > > > > I was using command > > "cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ > > -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' > Thanks, Mark! I get to know -D is a must for cmake to define variables. Best Qin > " > > and I thought the mvapich is compiled with --enable-shared... > > > > Could you give me some advice if possible? Thanks in advance. > > > > Best > > > > Qin > > -- > > 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] Error in Installing gromacs4.6.3 with mpi
Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': "/usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value " I was using command "cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' " and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- 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: Install gromacs4.6.3 with mpi
On Sat, Sep 7, 2013 at 4:55 PM, Qin Qiao wrote: > Dear all, > > I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster > and got the following error in step 'make': > > "/usr/bin/ld: > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation > R_X86_64_32 against `.bss' can not be used when making a shared object; > recompile with -fPIC > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad > value > " > > I was using command > "cmake .. -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ > -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' > Also with flag -DGMX_MPI=ON, sorry > " > and I thought the mvapich is compiled with --enable-shared... > > Could you give me some advice if possible? Thanks in advance. > > Best > Qin > -- 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] Install gromacs4.6.3 with mpi
Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': "/usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value " I was using command "cmake .. -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' " and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- 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] error while loading shared libraries: libgmx.so.6
Dear all, I'm using a c++ code to handle the xtc file with 'xtcio.h', but get the error when executing it. the command I use: g++ test.cpp -o test -I/usr/local/gromacs/include/gromacs -L/usr/local/gromacs/lib -lgmx ./test Error: ./test: error while loading shared libraries: libgmx.so.6: cannot open shared object file: No such file or directory But there's libgmx.so.6 in: /usr/local/gromacs/lib/libgmx.so.6 /usr/local/gromacs/lib/libgmx.so.6.0.0 Could you help me to see how to solve it? Best, Qin -- 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] How to install a new Forcefield in Gromacs 4.5.3
2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >><mailto:jalem...@vt.edu>>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> >> >> >> >> >> >> Qin Qiao wrote: >> >> Dear all, >> >> I would like to try a new forcefield in >> Gromacs >> 4.5.3. What >> should I do after I copied the ff to >> /share/gromacs/top >> directory? It seems the original FF.dat >> doesn't >> exist in >> 4.5.3.. >> Could you give me some help? >> >> >> pdb2gmx detects forcefield directories by >> searching >> for names >> that >> end in .ff, then looking in that directory for a >> "forcefield.doc" >> file that contains a brief description of the >>force field. >> >> -Justin >> >> >> Thanks. But I cannot find the new forcefield when >>I used >> pdb2gmx.. the folder of ff is named 'PACE.ff' >> >> >> It must also contain a forcefield.itp file to be >>recognized, and >> ultimately, to work at all. I did a test of minimum >> requirements, >> and only after I added a dummy forcefield.itp file to >>the test.ff >> subdirectory did pdb2gmx recognize the new force field. >> >> -Justin >> >> >> There is an .itp file in the ff.. but it doesn't work.. >> strange.. is there any other possibility? >> >> >> It works just fine for me. To be sure, I used the name >> "PACE.ff" >> instead of my generic "test.ff" to make sure capitalization or >> something foolish wasn't a problem. It worked fine, adding >>"PACE" >> as entry 16 in the pdb2gmx menu (I also have another custom >> force >> field, so the order of your pdb2gmx output may be different). >> >> The other thing to try is to build the force field in your >>working >> directory and see if pdb2gmx finds it there. This is, of >> course, >> not strictly required (and would be very inconvenient), but >>it could >> be a useful diagnostic. >> >> -Justin >> >> >>Thanks. But it doesn't work.. and I tried to copy the exact >>files in the charmm.ff to a new test.ff, and pdb2gmx doesn't >>find test.ff.. >> >> >>Do you have multiple versions of Gromacs on the same machine? If >>so, are you calling the right pdb2gmx? >> >> Could you tell me how can I tell which version of pdb2gmx I call? >> >> > pdb2gmx -h > > -Justin > > &
Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3
2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >><mailto:jalem...@vt.edu>>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> >> >> >> >> >> >> Qin Qiao wrote: >> >> Dear all, >> >> I would like to try a new forcefield in Gromacs >>4.5.3. What >> should I do after I copied the ff to >>/share/gromacs/top >> directory? It seems the original FF.dat doesn't >>exist in >> 4.5.3.. >> Could you give me some help? >> >> >> pdb2gmx detects forcefield directories by searching >>for names >> that >> end in .ff, then looking in that directory for a >>"forcefield.doc" >> file that contains a brief description of the force >> field. >> >> -Justin >> >> >> Thanks. But I cannot find the new forcefield when I used >> pdb2gmx.. the folder of ff is named 'PACE.ff' >> >> >> It must also contain a forcefield.itp file to be recognized, and >> ultimately, to work at all. I did a test of minimum >>requirements, >> and only after I added a dummy forcefield.itp file to the >> test.ff >> subdirectory did pdb2gmx recognize the new force field. >> >> -Justin >> >> >>There is an .itp file in the ff.. but it doesn't work.. >>strange.. is there any other possibility? >> >> >>It works just fine for me. To be sure, I used the name "PACE.ff" >>instead of my generic "test.ff" to make sure capitalization or >>something foolish wasn't a problem. It worked fine, adding "PACE" >>as entry 16 in the pdb2gmx menu (I also have another custom force >>field, so the order of your pdb2gmx output may be different). >> >>The other thing to try is to build the force field in your working >>directory and see if pdb2gmx finds it there. This is, of course, >>not strictly required (and would be very inconvenient), but it could >>be a useful diagnostic. >> >>-Justin >> >> >> Thanks. But it doesn't work.. and I tried to copy the exact files in the >> charmm.ff to a new test.ff, and pdb2gmx doesn't find test.ff.. >> >> > Do you have multiple versions of Gromacs on the same machine? If so, are > you calling the right pdb2gmx? > > Could you tell me how can I tell which version of pdb2gmx I call? -Justin > > > >> Best, >> >> Qin >> >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> >><http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >><mailto:gmx-users@gromacs.org>>> >&g
Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3
2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul ><mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> >><mailto:jalem...@vt.edu>>> >> >> >> >> >> Qin Qiao wrote: >> >> Dear all, >> >> I would like to try a new forcefield in Gromacs 4.5.3. What >> should I do after I copied the ff to /share/gromacs/top >> directory? It seems the original FF.dat doesn't exist in >>4.5.3.. >> Could you give me some help? >> >> >> pdb2gmx detects forcefield directories by searching for names >>that >> end in .ff, then looking in that directory for a >> "forcefield.doc" >> file that contains a brief description of the force field. >> >> -Justin >> >> >>Thanks. But I cannot find the new forcefield when I used >>pdb2gmx.. the folder of ff is named 'PACE.ff' >> >> >>It must also contain a forcefield.itp file to be recognized, and >>ultimately, to work at all. I did a test of minimum requirements, >>and only after I added a dummy forcefield.itp file to the test.ff >>subdirectory did pdb2gmx recognize the new force field. >> >>-Justin >> >> >> There is an .itp file in the ff.. but it doesn't work.. strange.. is there >> any other possibility? >> >> > It works just fine for me. To be sure, I used the name "PACE.ff" instead > of my generic "test.ff" to make sure capitalization or something foolish > wasn't a problem. It worked fine, adding "PACE" as entry 16 in the pdb2gmx > menu (I also have another custom force field, so the order of your pdb2gmx > output may be different). > > The other thing to try is to build the force field in your working > directory and see if pdb2gmx finds it there. This is, of course, not > strictly required (and would be very inconvenient), but it could be a useful > diagnostic. > > -Justin > > >> Thanks. But it doesn't work.. and I tried to copy the exact files in the charmm.ff to a new test.ff, and pdb2gmx doesn't find test.ff.. > Best, >> >> Qin >> >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-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 >><mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>
Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3
2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I would like to try a new forcefield in Gromacs 4.5.3. What >>should I do after I copied the ff to /share/gromacs/top >>directory? It seems the original FF.dat doesn't exist in 4.5.3.. >>Could you give me some help? >> >> >>pdb2gmx detects forcefield directories by searching for names that >>end in .ff, then looking in that directory for a "forcefield.doc" >>file that contains a brief description of the force field. >> >>-Justin >> >> >> Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the >> folder of ff is named 'PACE.ff' >> > > It must also contain a forcefield.itp file to be recognized, and > ultimately, to work at all. I did a test of minimum requirements, and only > after I added a dummy forcefield.itp file to the test.ff subdirectory did > pdb2gmx recognize the new force field. > > -Justin > > >> There is an .itp file in the ff.. but it doesn't work.. strange.. is there any other possibility? > >>Best, >> >>Qin >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-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 >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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] How to install a new Forcefield in Gromacs 4.5.3
2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I would like to try a new forcefield in Gromacs 4.5.3. What should I do >> after I copied the ff to /share/gromacs/top directory? It seems the original >> FF.dat doesn't exist in 4.5.3.. Could you give me some help? >> >> > pdb2gmx detects forcefield directories by searching for names that end in > .ff, then looking in that directory for a "forcefield.doc" file that > contains a brief description of the force field. > > -Justin > Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the folder of ff is named 'PACE.ff' > > Best, >> >> Qin >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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] How to install a new Forcefield in Gromacs 4.5.3
Dear all, I would like to try a new forcefield in Gromacs 4.5.3. What should I do after I copied the ff to /share/gromacs/top directory? It seems the original FF.dat doesn't exist in 4.5.3.. Could you give me some help? Best, Qin -- 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] To make continuous trj in REMD
2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/7 Justin A. Lemkul > <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> <mailto:jalem...@vt.edu>>> >> >> >> >> >> Qin Qiao wrote: >> >> Dear all, >> >> I came across a problem when I want to make the REMD >> trajectories continuous. >> >> What I did: >> >> 1. 'demux.pl <http://demux.pl> <http://demux.pl> >> <http://demux.pl> REMD_0.log' --to get the >> 'replica_index.xvg' >> >> >> 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux >> ../replica_index.xvg' >> >> It seems smooth. But when I check the rmsd of the output >> 0_resort.xtc, I found it's still discontinuous.. with big >> jumps >> about 0.5nm..! Could you help me to figure out what's wrong? >> Thanks a lot. >> It has been solved. The reason is for the order of the xtc file in trjcat. I should use -f ../REMD_?.xtc ../REMD_??.xtc to get the correct order, or it will be mixed. Many thanks to Prof. Spoel! >> >> Have you properly accounted for periodicity effects? >> >> -Justin >> >> >> It's the same after I remove periodicity by trjconv -pbc mol -ur >> compact ... >> >> >> One iteration of trjconv is not necessarily enough to produce a >> properly imaged trajectory. What is going on in the trajectory when >> these spikes are occurring? >> >> -Justin >> >> In VMD, it just seems to change to a different conformation... >> > > Then it sounds like something has gone wrong with the demultiplexing. As for > what that is, it's hard to say. Look into the .log file and resulting .xvg > file (from demux.pl) to make sure that the proper exchanges were identified. > Then try to determine from which replica that sudden change arose (i.e., in > which of the original trajectories was that configuration present). Finding > it should be relatively easy; just dump out the frames at that time point > from each of the trajectories to see. > > For further troubleshooting, it would also be useful to know your Gromacs > version, in case there is some sort of bug. It is too early to tell, though, > where the problem lies. > > -Justin > >> Best, >> >> Qin >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- gmx-users mailing list gmx-us...@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >&g
Re: [gmx-users] Nose-hoover T-coupling in REMD
2010/12/26 ms > On 25/12/10 02:12, Qin Qiao wrote: >>> >>> Thanks a lot! >>>> >>>> It says Nose-hoover coupling generates the correct canonical ensemble, >>>> and >>>> that's the reason why I used it. I wonder whether v-rescale can also get >>>> the >>>> correct ensemble. Could you tell me? >>>> >>>> >>> As far as I know v-rescale should generate a correct ensemble. >>> >> > On 25/12/10 12:40, Qin Qiao wrote: > > I'm not sure, since actually kinetic energy should have fluctuation, and > the > > v-rescaling may suppress the fluctuation.. > > > > (PLEASE don't top post!!) > > Well, the thermostat author, who I happen to know, says it generates the > right ensemble. :) I'm not an expert so I can't say if it's true, but if you > like you can read the original papers, linked here: > > > http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the > > cheers, > > m. > > Thanks a lot! Qin > -- > Massimo Sandal, Ph.D. > http://devicerandom.org > -- > 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] To make continuous trj in REMD
2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I came across a problem when I want to make the REMD >>trajectories continuous. >> >>What I did: >> >>1. 'demux.pl <http://demux.pl> <http://demux.pl> REMD_0.log' >> --to get the 'replica_index.xvg' >> >> >>2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux >>../replica_index.xvg' >> >>It seems smooth. But when I check the rmsd of the output >>0_resort.xtc, I found it's still discontinuous.. with big jumps >>about 0.5nm..! Could you help me to figure out what's wrong? >>Thanks a lot. >> >> >>Have you properly accounted for periodicity effects? >> >>-Justin >> >> >> It's the same after I remove periodicity by trjconv -pbc mol -ur compact >> ... >> >> > > One iteration of trjconv is not necessarily enough to produce a properly > imaged trajectory. What is going on in the trajectory when these spikes are > occurring? > > -Justin > > In VMD, it just seems to change to a different conformation... Best, >> >>Qin >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-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 >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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] To make continuous trj in REMD
2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I came across a problem when I want to make the REMD trajectories >> continuous. >> >> What I did: >> >> 1. 'demux.pl <http://demux.pl> REMD_0.log' --to get the >> 'replica_index.xvg' >> >> 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' >> >> It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I >> found it's still discontinuous.. with big jumps about 0.5nm..! Could you >> help me to figure out what's wrong? Thanks a lot. >> >> > Have you properly accounted for periodicity effects? > > -Justin > It's the same after I remove periodicity by trjconv -pbc mol -ur compact ... > Best, >> >> Qin >> >> -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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] To make continuous trj in REMD
Dear all, I came across a problem when I want to make the REMD trajectories continuous. What I did: 1. 'demux.pl REMD_0.log' --to get the 'replica_index.xvg' 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I found it's still discontinuous.. with big jumps about 0.5nm..! Could you help me to figure out what's wrong? Thanks a lot. Best, Qin -- 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] Nose-hoover T-coupling in REMD
I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. 2010/12/25 ms > On 25/12/10 02:12, Qin Qiao wrote: > >> Thanks a lot! >> >> It says Nose-hoover coupling generates the correct canonical ensemble, and >> that's the reason why I used it. I wonder whether v-rescale can also get >> the >> correct ensemble. Could you tell me? >> > > As far as I know v-rescale should generate a correct ensemble. > > > -- > Massimo Sandal, Ph.D. > http://devicerandom.org > -- > 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] Nose-hoover T-coupling in REMD
Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Best, Qin 2010/12/25 David van der Spoel > On 12/24/10 6:40 PM, ms wrote: > >> On 24/12/10 12:26, David van der Spoel wrote: >> >> I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong >>> ensemble but it also biases the energy distribution to lower energies. >>> >> >> Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to >> less confusion if it is removed? :) >> >> It's still useful for equilibration, e.g. gas to liquid conversion. > > -- > David. > > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se > > > -- > 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] Nose-hoover T-coupling in REMD
Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could do it by setting tau_t small in the Nose-hoover T coupling, but there will come the warning in Gromacs. I maxwarned the warning to proceed, and find the temperature is ok, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks a lot. Best, Qin 2010/12/21 Qin Qiao > Dear all, > > I wonder what will happen in Nose-hoover coupling when tau_t = dt * > nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the > Gromacs warning) > > I tried this setting, to find the temperature is OK, but I am not sure > whether it will introduce some artifacts in the simulation and what kind of > artifacts. Could you tell me? Thanks in advance. > > Best, > > Qin > > > -- 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] Nose-hoover T-coupling nsttcouple
Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation and what kind of artifacts. Could you tell me? Thanks in advance. Best, Qin -- 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] Question about Extention simulation in REMD
Thanks! It really is. For the input cpt may have been overwritten before, when I put it in mdrun again.. 2010/12/17 Mark Abraham > > > On 12/17/10, *Qin Qiao * wrote: > > Thanks! > > But still sth strange: I found the total energy is not identical between > the last frame of the previous REMD and the first frame of the next REMD in > one replica. > > last frame of the previous: 500.00 -372343.906250 > first frame of the next: 0.00 -361778.375000 > > I wonder whether there's some problem and what caused it.. > > > OK, we'll need to see the exact sequence of commands that produced your > observations, i.e. mdrun, then tpbconv, then mdrun. The fact that you're > managing to get the time reset to zero indicates you've done something > wrong. As a guess, you didn't use the right .cpt file with the second mdrun > -cpi. > > > > > My setting > In the .mdp of the previous simulation, gen_vel was on; I didn't record the > velocity by putting nstvout =0; I used xtcgrp = Protein. > > > These don't matter. > > Mark > > > > Best > > Qin > > 2010/12/15 Justin A. Lemkul > >> >> >> >> Qin Qiao wrote: >> >>> Dear Sir or Madam, >>> >>> I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. >>> Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. >>> I couldn't do it by >>> >>> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr >>> >>> mdrun -s next.tpr -cpi previous.cpt >>> >>> >>> I guess it's not for an iterative line in the answer in >>> http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since >>> the mdrun should run simultaneously. >>> >>> >> The iterative approach Mark describes in that post is for the tpbconv >> step. Simply extend all of your .tpr files to generate new ones (iterate >> over all your .tpr files), then proceed with mdrun as you would normally, >> making use of the -cpi feature. >> >> -Justin >> >> >> Could you give some advice? Thanks. >>> >>> Best, >>> >>> Qin >>> >>> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> 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
Re: [gmx-users] Question about Extention simulation in REMD
Thanks! But still sth strange: I found the total energy is not identical between the last frame of the previous REMD and the first frame of the next REMD in one replica. last frame of the previous: 500.00 -372343.906250 first frame of the next: 0.00 -361778.375000 I wonder whether there's some problem and what caused it.. My setting In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. Best Qin 2010/12/15 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear Sir or Madam, >> >> I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. >> Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. >> I couldn't do it by >> >> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr >> >> mdrun -s next.tpr -cpi previous.cpt >> >> >> I guess it's not for an iterative line in the answer in >> http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since >> the mdrun should run simultaneously. >> >> > The iterative approach Mark describes in that post is for the tpbconv step. > Simply extend all of your .tpr files to generate new ones (iterate over all > your .tpr files), then proceed with mdrun as you would normally, making use > of the -cpi feature. > > -Justin > > > Could you give some advice? Thanks. >> >> Best, >> >> Qin >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > 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] Question about Extention simulation in REMD
Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I guess it's not for an iterative line in the answer in http://www.mail-archive.com/gmx-users@gromacs.org/msg33566.html, since the mdrun should run simultaneously. Could you give some advice? Thanks. Best, Qin -- 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
