[gmx-users] random seed in molecular dynamics
hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -thanks -- 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 after trjconf processing
Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb: 0.241, 0.237 nm Why this error have occurred (with no minimized conformers) and how it could be fixed correctly ? James -- 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] constant protonation state MD
There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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] random seed in molecular dynamics
If I recall correctly it uses the seed provided in the mdp file. If no seed is provided it uses the process id for seeding. The manual explains the details. Erik On 3 May 2013, at 08:00, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -thanks -- 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] Error after trjconf processing
Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb: 0.241, 0.237 nm Why this error have occurred (with no minimized conformers) and how it could be fixed correctly ? James -- 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] random seed in molecular dynamics
gen_vel controls the generation of random velocities. grompp follows it (but I'd have to check the code to see what it does if you use grompp -t). tprconv does not follow it. The random seed is in a different variable, but only does anything if gen_vel=yes. I am not sure what the basis of your confusion about repeated calls to grompp is. Mark On Fri, May 3, 2013 at 8:00 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: hey this is regarding random seed used in md.this is when it selects the intial velocity and selects from maxwell-istribution.but is it selects only once or selects this random seed every time when grompp makes .tpr file.really confused about this random seed concept.can u clear my confusion?? -thanks -- 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] Error after trjconf processing
Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings 2013/5/3 Mark Abraham mark.j.abra...@gmail.com Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb: 0.241, 0.237 nm Why this error have occurred (with no minimized conformers) and how it could be fixed correctly ? James -- 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] installation Gromacs-Fedora18
Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library
[gmx-users] Simulation of Small Water Box
Dear Users Can Anybody help me to simulate a water box with nearly 14.45 A box size and approximately 93 water molecules. I have tried to simulate it using the 'spc' water model. I have done the SD and CG minimization step. Till that step it was fine, but when I tried to do MD then I got the following error message *One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.* Is there any well established method to simulate a small water box nearly of the size I have mentioned? It would be great if I could get it. Have a nice day. -- With Regards Monoj Mon Kalita Institute of Biophotonicshttp://www.ym.edu.tw/biophotonics/eng_version/home.htm National Yang-Ming Universityhttp://nymu-e.web.ym.edu.tw/front/bin/home.phtml Taipei, Taiwan -- 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] installation Gromacs-Fedora18
On 5/3/13 5:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux
Re: [gmx-users] Simulation of Small Water Box
On 5/3/13 5:41 AM, Monoj Mon Kalita wrote: Dear Users Can Anybody help me to simulate a water box with nearly 14.45 A box size and approximately 93 water molecules. I have tried to simulate it using the 'spc' water model. I have done the SD and CG minimization step. Till that step it was fine, but when I tried to do MD then I got the following error message *One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.* Is there any well established method to simulate a small water box nearly of the size I have mentioned? It would be great if I could get it. Have a nice day. The error warns you that you are violating the minimum image convention. For a system of such a tiny size, fluctuations in the box vectors that arise from pressure coupling can be quite significant. Unless you are using a cutoff of 0.7 nm or less (which would be incorrect to do, as you will have serious cutoff errors), you cannot use a box this small. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] installation Gromacs-Fedora18
this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw (you can put it where you want) be sure to enable shared because gromacs seems need it if you want double precision remove --enable-float gromacs 4.5.5 cd to folder ./configure CPPFLAGS=-I/usr/local/fftw/include LDFLAGS=-L/usr/localfftw/lib --with-fft=fftw3 make make install make clean --disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++
Re: [gmx-users] distance of pull group 1 is larger than the box size
On 5/3/13 12:10 AM, Arunima Shilpi wrote: Hello sir I got the following error while running pulling mdrun -s pull.tpr distance of pull group 1 is larger than the box size I request you to kindly guide me in overcoming the error Since we know nothing of what you are doing or how you are doing it, there's very little advice anyone can give. Your pull settings are inconsistent with your configuration, or the system has blown up, causing pull_group1 to go flying out of the box. Please provide more detail, and in particular consult http://www.catb.org/~esr/faqs/smart-questions.html. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Proteins with ADP ATP cofactors
Dear all, Does anybody have the parameters files for ATP and ADP for the AMBER03 ff? Alternatively, I know that I can find the corresponding files on the AMBER package web-site http://www.pharmacy.manchester.ac.uk/bryce/amber#cof but I don't know how convert these files so I can use them with GROMACS. There are several emails on this mailing-list concerning my request, but I can't find a reply which clearly address the problem. Thank you -- 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 replica exchange
Summarizing! On Fri, May 3, 2013 at 12:31 AM, XAvier Periole x.peri...@rug.nl wrote: Are confirming that you reproduce the problem with gmx-4.6.1 or simply summarizing in case we lose track :)) On May 2, 2013, at 23:31, Michael Shirts mrshi...@gmail.com wrote: So to summarize -- the problem appears to be with particle decomposition. On Thu, May 2, 2013 at 4:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. Mark -- 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 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
Re: [gmx-users] installation Gromacs-Fedora18
many thanks to you all, I did installation as root it works well I like gromacs users discussion. It is very useful :) On 3 May 2013 19:10, Francesco frac...@myopera.com wrote: this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw (you can put it where you want) be sure to enable shared because gromacs seems need it if you want double precision remove --enable-float gromacs 4.5.5 cd to folder ./configure CPPFLAGS=-I/usr/local/fftw/include LDFLAGS=-L/usr/localfftw/lib --with-fft=fftw3 make make install make clean --disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes
Re: [gmx-users] Error after trjconf processing
On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.comwrote: Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags I didn't see anything like that in this thread... (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? Don't know. Look at your files and see what's there :-) so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings The PBC was always there. The question is likely whether the code assumes molecules have coordinates that do not straddle the current box, or not. mdrun goes to the expense of ensuring that it does it correctly, but there are countless other points where the code may or may not still be doing something that was correct at some point in the last 15 years under certain assumptions, but may not be correct now or under new conditions... Mark 2013/5/3 Mark Abraham mark.j.abra...@gmail.com Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb: 0.241, 0.237 nm Why this error have occurred (with no minimized conformers) and how it could be fixed correctly ? James -- 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 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
[gmx-users] Re: rotation of a ligand
Dear users, I tried to calculate the order parameter of benzene ring of the ligand using g_order but I have a error as the following : make_ndx -f topol.tpr -o order.xvg a C1 C2 C3 C4 C5 C6 Found 6 atoms with names C1 C2 C3 C4 C5 C6 26 C1_C2_C3_C4_C5_C6 : 6 atoms q g_order -f traj.xtc -s topol.tpr -n order.ndx -order.xvg Fatal error: grp 1 does not have same number of elements as grp 1 What should I do? 2013/5/3 Ahmet yıldırım ahmedo...@gmail.com Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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] constant protonation state MD
Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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] Error after trjconf processing
I've noticed that the minimized conformers no longer has the velocities in gro file (and npt rus without warnings in that case) in comparison to the not-minimized structures ( where velocities were present and gromp sent warnings). All pbc options lare the same for all conformers and box vectors correctly defined in boundary regions. But after npt equilibration of the minimized structures ( velocities again present in the gro file) my system have crushed at the beginning of the production run. So the problem in the velocities set which wre taken from the initial pulling run (the same for each conformers). Should I re-assign velocities for each conformer (addition nvt run) to fix it ? James 2013/5/3 Mark Abraham mark.j.abra...@gmail.com On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.com wrote: Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags I didn't see anything like that in this thread... (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? Don't know. Look at your files and see what's there :-) so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings The PBC was always there. The question is likely whether the code assumes molecules have coordinates that do not straddle the current box, or not. mdrun goes to the expense of ensuring that it does it correctly, but there are countless other points where the code may or may not still be doing something that was correct at some point in the last 15 years under certain assumptions, but may not be correct now or under new conditions... Mark 2013/5/3 Mark Abraham mark.j.abra...@gmail.com Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb: 0.241, 0.237 nm Why this error have occurred (with no minimized conformers) and how it could be fixed correctly ? James -- 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
Re: [gmx-users] constant protonation state MD
I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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 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 after trjconf processing
EM has no velocities, by definition. Does the EM mdrun write a .gro file with velocities? If so, that's a bug. On Fri, May 3, 2013 at 2:51 PM, James Starlight jmsstarli...@gmail.comwrote: I've noticed that the minimized conformers no longer has the velocities in gro file (and npt rus without warnings in that case) in comparison to the not-minimized structures ( where velocities were present and gromp sent warnings). All pbc options lare the same for all conformers and box vectors correctly defined in boundary regions. But after npt equilibration of the minimized structures ( velocities again present in the gro file) my system have crushed at the beginning of the production run. So the problem in the velocities set which wre taken from the initial pulling run (the same for each conformers). Huh? After EM there should be no velocities, and you should instruct the grompp before your equilibration to generate new ones regardless. Should I re-assign velocities for each conformer (addition nvt run) to fix it ? There seems to be no purpose to trying to start a new simulation from some configuration, doing EM on it, and then trying to equilibrate starting with the pre-EM velocities (even if it is possible, which I do not think it should be). The energy distributions are guaranteed to be mutually inconsistent. Mark James 2013/5/3 Mark Abraham mark.j.abra...@gmail.com On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.com wrote: Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags I didn't see anything like that in this thread... (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? Don't know. Look at your files and see what's there :-) so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings The PBC was always there. The question is likely whether the code assumes molecules have coordinates that do not straddle the current box, or not. mdrun goes to the expense of ensuring that it does it correctly, but there are countless other points where the code may or may not still be doing something that was correct at some point in the last 15 years under certain assumptions, but may not be correct now or under new conditions... Mark 2013/5/3 Mark Abraham mark.j.abra...@gmail.com Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb: 8.895, 8.474 nm WARNING 1 [file ./mdps/minim.mdp]: The sum of the two largest charge group radii (17.368397) is larger than rlist (1.00) Finally after minimization of each conformer with the same R_list (with maxwarn 1 flag) and starting new MD on the minimizing conformer I have no such error: Largest charge group radii for Van der Waals: 0.241, 0.237 nm Largest charge group radii for Coulomb:
Re: [gmx-users] Error after trjconf processing
Mark, but if I run npt equilibration onto minimized structure (without velocities) without definition of the new velocities in the npt.mdp file gen_vel = No I noticed that in npt.gro file velocities present. Have it been assigned inspite on gen_vel = No in mdp? James 2013/5/3 Mark Abraham mark.j.abra...@gmail.com EM has no velocities, by definition. Does the EM mdrun write a .gro file with velocities? If so, that's a bug. On Fri, May 3, 2013 at 2:51 PM, James Starlight jmsstarli...@gmail.com wrote: I've noticed that the minimized conformers no longer has the velocities in gro file (and npt rus without warnings in that case) in comparison to the not-minimized structures ( where velocities were present and gromp sent warnings). All pbc options lare the same for all conformers and box vectors correctly defined in boundary regions. But after npt equilibration of the minimized structures ( velocities again present in the gro file) my system have crushed at the beginning of the production run. So the problem in the velocities set which wre taken from the initial pulling run (the same for each conformers). Huh? After EM there should be no velocities, and you should instruct the grompp before your equilibration to generate new ones regardless. Should I re-assign velocities for each conformer (addition nvt run) to fix it ? There seems to be no purpose to trying to start a new simulation from some configuration, doing EM on it, and then trying to equilibrate starting with the pre-EM velocities (even if it is possible, which I do not think it should be). The energy distributions are guaranteed to be mutually inconsistent. Mark James 2013/5/3 Mark Abraham mark.j.abra...@gmail.com On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.com wrote: Mark, thanks for suggestions as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc nojump flags I didn't see anything like that in this thread... (the same way I found in Justin's umbrella tutorial where conformers were extracted from pulling trajectory). Might it be source of the some artifacts with pbc ? Don't know. Look at your files and see what's there :-) so if I understood correctly subsequent minimization (with maxwarn 1 flag) restored original pbc (based on box vectors defined in gro file ) because in next production MD there were no warnings The PBC was always there. The question is likely whether the code assumes molecules have coordinates that do not straddle the current box, or not. mdrun goes to the expense of ensuring that it does it correctly, but there are countless other points where the code may or may not still be doing something that was correct at some point in the last 15 years under certain assumptions, but may not be correct now or under new conditions... Mark 2013/5/3 Mark Abraham mark.j.abra...@gmail.com Trajectory frames written by mdrun are not post-processed to guess how you would like PBC to be treated for whatever purpose you have next. So if a molecule straddles a periodic boundary given the current center position, that's what it looks like. If there are things you want to do, then there's the instructions at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . In turn, it seems grompp applies a whole collection of basic checks, and it seems that one of them might not be sufficiently PBC-aware. Such checks appropriate for a normal grompp workflow, where this is the first point the GROMACS machinery gets to see what you intend to do and is the point where it can help you ensure sanity. It seems there's room for a small improvement, too. If the subsequent MD works, then you need have no concern, but if you want to post-process your trjconv frames so that the molecules are whole, you will suppress this warning the correct way. Mark On Fri, May 3, 2013 at 8:18 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have performed long md run. From the production trajectory by means of trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract conformers from first 300 ps each 10ps steps I've extracted 10 conformers in the desired time step Than when I perform MD on each conformer I obtain error (when I loaded in grompp conformer from the initial run I have no such error) Number of degrees of freedom in T-Coupling group rest is 130551.00 Largest charge group radii for Van der Waals: 8.895, 7.586 nm Largest charge group radii for Coulomb:
Re: [gmx-users] Error after trjconf processing
On Fri, May 3, 2013 at 3:17 PM, James Starlight jmsstarli...@gmail.comwrote: Mark, but if I run npt equilibration onto minimized structure (without velocities) without definition of the new velocities in the npt.mdp file gen_vel = No I noticed that in npt.gro file velocities present. Have it been assigned inspite on gen_vel = No in mdp? I can't answer - I don't know from your description and filename what was in 1) the coordinte file you input to the EM grompp, 2) the .gro file you got out of EM mdrun (which presumably went into the NPT grompp), 3) the .tpr file you got out of NPT grompp, and 4) the .gro file you got out of NPT mdrun (which will always have velocities regardless of the foregoing) Please respect your reader's time and describe your observations carefully :-) I think there should never be velocities in 2. Velocities in 3 should follow what the .mdp file said (but if 2 wrote velocities, then it is conceivable that those are still the velocities in 3 iff gen_vel=no, but you would have to inspect the values with gmxdump to see what was happening). Mark -- 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] constant protonation state MD
If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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 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] Re: installation Gromacs-Fedora18
Date: Fri, 3 May 2013 20:00:57 +0900 From: Souilem Safa safasouil...@gmail.com Subject: Re: [gmx-users] installation Gromacs-Fedora18 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cagkn4tm30mse2z0wcsqabwumeiswt-p+qbuo0wantgep9qf...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 many thanks to you all, I did installation as root it works well If you have root rights, why don't you just install Fedora's gromacs package? $ yum install gromacs Cheers, Christoph I like gromacs users discussion. It is very useful :) On 3 May 2013 19:10, Francesco frac...@myopera.com wrote: this is what I do to install gromacs 4.5.5 on fedora 18 fftw libraries cd fftw-3.3.3_folder ./configure --enable-threads --enable-shared --enable-float --prefix=/usr/local/fftw make make install make clean in this way I install single precision (--enable-float) fftw libraries in /usr/local/fftw (you can put it where you want) be sure to enable shared because gromacs seems need it if you want double precision remove --enable-float gromacs 4.5.5 cd to folder ./configure CPPFLAGS=-I/usr/local/fftw/include LDFLAGS=-L/usr/localfftw/lib --with-fft=fftw3 make make install make clean --disable-float for double precision and --enable-mpi if you need mpi remember that fftw and gromacs must have the same precision. hope this helps you cheers Francesco On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS=-L/home/safa/fftw-3.3.2/lib CPPFLAGS=-I/home/safa/programs/fftw-3.3.2/include --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is
[gmx-users] Re: where can be obtain circled lipids bilayer? (Björn Sommer)
Hello Albert, our MembraneEditor (Java Webstart) http://cm2.cellmicrocosmos.org has a new plugin available which can be used to build vesicle membranes. http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=35t=676 You have to import it into the MembraneEditor by using Settings - Manage Plugin Algorithms. The VesicleBuilder is a beta version, but it is quite easy to use. Especially, it is easy to combine it with your own PDB files. Just look at the tutorials and documentation. Here are some videos: http://www.cellmicrocosmos.org/index_cm2.php?inputPage=cm2videos The approach might be more easy for you than using PackMol. Best wishes, Björn Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- 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] genion
Hi, Just wondering. My system shows this: System has non-zero total charge: 11.98 and thus, I use the command as below to add 12 Cl to the protein: genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12 However, when I checked the genion.log file, it shows that the system has total charge of 12. Isn't it supposed to be 0? This is what the genion.log shows: Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Using shifted Lennard-Jones, switch between 0 and 1 nm Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 12.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC-like water optimization for 3745014 molecules. Thank you. Best regards, -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Comparing Charmm 27 energies from GROMACS and NAMD
Thanks Mark! No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. The rerun option is interesting - in my case however the potential energy terms stayed identical but the kinetic term became zero. Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. I totally agree :) So far I found out that for no cut-off simulation in Gromacs, rather that specifying a large cut-off, it needs rlist=rvdw=rcoulomb=0 and pbc=no along with ns_type=simple and nstlist=0 (according to the manual). I am running various tests and will update if I find out what is causing the discrepancy. Reza On May 1, 2013, at 5:46 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 1, 2013 at 2:32 PM, Reza Salari resa...@gmail.com wrote: Hi Justin, I actually did :) but it ended up being bigger than 50 kb so it needed moderator approval to show up. I was hoping it would've been released by now. I'll attach a the details below. Any help/hint is highly appreciated. Reza Details: *1)* Both systems were prepared using VMD membrane package and then waters were removed. I used Gromacs 4.6.1 and NAMD 2.9. *2)* Simulations were run in vacuum as a single-point energy calculations (0 step). No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. PME was not used. *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the output was saved as the pdb format. The mdp file: integrator= md nsteps= 0 nstlog = 1 nstlist= 1 ns_type= grid rlist= 100.0 coulombtype= cut-off rcoulomb= 100.0 rvdw= 100.0 pbc = no *4) *NAMD input file: structure ../0_prep/memb_nowat.psf paratypecharmm on parameterspar_all27_prot_lipid.prm exclude scaled1-4 1-4scaling 1.0 switching off switchdist 8 cutoff 1000 pairlistdist 1000 margin 0 timestep 1.0 outputenergies 1 outputtiming 1 binaryoutput no coordinates ../0_prep/memb_nowat.pdb outputname out dcdfreq 10 temperature 300 run 0 *5)* Energies: For Single POPC (kcal/mol) Gromacs NAMD Diff Bond 43.0022 43.0015 -0.0007 Angle 80.6568 80.6571 0.0003 Dih 29.8083 29.8083 0. Imp 0.8452 0.8452 0. Coul -17.2983 -17.2983 0. LJ -7.0798 -7.0798 0. Pot 129.9343 129.9340 -0.0003 The intra-molecule terms look fine. Since this is a lipid, there are non-bonded interactions that are intra-molecule, so the non-bondeds also seem fine. For POPC Memb (kcal/mol) Gromacs NAMD Diff Bond 1539.1181 1539.1162 -0.0019 Angle 3111.9264 3111.9197 -0.0067 Dih 1250.5425 1250.5421 -0.0004 Imp 16.2837 16.2837 0. Coul -1837.8585 -1705.3075 132.5510 LJ -995.0311 -1219.3432 -224.3121 Pot 3084.9904 2993.2110 -91.7794 Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. Mark On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) It appears you hit send too early. Please provide the entirety of the details you intended. Complete .mdp files and actual quantification of the differences you are observing are also very important. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**
Re: [gmx-users] genion
On 5/3/13 11:27 AM, Ewaru wrote: Hi, Just wondering. My system shows this: System has non-zero total charge: 11.98 and thus, I use the command as below to add 12 Cl to the protein: genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn 12 However, when I checked the genion.log file, it shows that the system has total charge of 12. Isn't it supposed to be 0? This is what the genion.log shows: The charge that genion reports is the one that it finds in the system contained in the .tpr file. grompp reports a net charge of 12 (or close enough to it, see http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) and genion confirms that is what it finds. The next invocation of grompp will confirm that your net charge is zero. -Justin Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Using shifted Lennard-Jones, switch between 0 and 1 nm Cut-off's: NS: 1 Coulomb: 1 LJ: 1 System total charge: 12.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ12. Tabscale = 500 points/nm Enabling SPC-like water optimization for 3745014 molecules. Thank you. Best regards, -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD
On 5/3/13 11:33 AM, Reza wrote: Thanks Mark! No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. The rerun option is interesting - in my case however the potential energy terms stayed identical but the kinetic term became zero. If you are using an .xtc file for the rerun, this makes sense since the .xtc does not store velocities and hence kinetic energy cannot be calculated. -Justin Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. I totally agree :) So far I found out that for no cut-off simulation in Gromacs, rather that specifying a large cut-off, it needs rlist=rvdw=rcoulomb=0 and pbc=no along with ns_type=simple and nstlist=0 (according to the manual). I am running various tests and will update if I find out what is causing the discrepancy. Reza On May 1, 2013, at 5:46 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 1, 2013 at 2:32 PM, Reza Salari resa...@gmail.com wrote: Hi Justin, I actually did :) but it ended up being bigger than 50 kb so it needed moderator approval to show up. I was hoping it would've been released by now. I'll attach a the details below. Any help/hint is highly appreciated. Reza Details: *1)* Both systems were prepared using VMD membrane package and then waters were removed. I used Gromacs 4.6.1 and NAMD 2.9. *2)* Simulations were run in vacuum as a single-point energy calculations (0 step). No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. PME was not used. *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the output was saved as the pdb format. The mdp file: integrator= md nsteps= 0 nstlog = 1 nstlist= 1 ns_type= grid rlist= 100.0 coulombtype= cut-off rcoulomb= 100.0 rvdw= 100.0 pbc = no *4) *NAMD input file: structure ../0_prep/memb_nowat.psf paratypecharmm on parameterspar_all27_prot_lipid.prm exclude scaled1-4 1-4scaling 1.0 switching off switchdist 8 cutoff 1000 pairlistdist 1000 margin 0 timestep 1.0 outputenergies 1 outputtiming 1 binaryoutput no coordinates ../0_prep/memb_nowat.pdb outputname out dcdfreq 10 temperature 300 run 0 *5)* Energies: For Single POPC (kcal/mol) Gromacs NAMD Diff Bond 43.0022 43.0015 -0.0007 Angle 80.6568 80.6571 0.0003 Dih 29.8083 29.8083 0. Imp 0.8452 0.8452 0. Coul -17.2983 -17.2983 0. LJ -7.0798 -7.0798 0. Pot 129.9343 129.9340 -0.0003 The intra-molecule terms look fine. Since this is a lipid, there are non-bonded interactions that are intra-molecule, so the non-bondeds also seem fine. For POPC Memb (kcal/mol) Gromacs NAMD Diff Bond 1539.1181 1539.1162 -0.0019 Angle 3111.9264 3111.9197 -0.0067 Dih 1250.5425 1250.5421 -0.0004 Imp 16.2837 16.2837 0. Coul -1837.8585 -1705.3075 132.5510 LJ -995.0311 -1219.3432 -224.3121 Pot 3084.9904 2993.2110 -91.7794 Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. Mark On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) It appears you hit send too early. Please provide the entirety of the details you intended. Complete .mdp files and actual quantification of the differences you are observing are also very important. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search
Re: [gmx-users] Re: rotation of a ligand
On 5/3/13 7:56 AM, Ahmet yıldırım wrote: Dear users, I tried to calculate the order parameter of benzene ring of the ligand using g_order but I have a error as the following : make_ndx -f topol.tpr -o order.xvg a C1 C2 C3 C4 C5 C6 Found 6 atoms with names C1 C2 C3 C4 C5 C6 26 C1_C2_C3_C4_C5_C6 : 6 atoms q g_order -f traj.xtc -s topol.tpr -n order.ndx -order.xvg Fatal error: grp 1 does not have same number of elements as grp 1 g_order calculates order parameters for lipid acyl chains and thus is not applicable here. What should I do? Consult Chapter 8 of the manual to see if there is a program that is capable of calculating the quantity you are interested in. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: genion
Hi Justin, Thank you for your prompt reply! My grompp goes like this: grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: Fatal error: 2 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. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; and thus I was checking if my ions are neutralised or not. Thanking you in advance. Best regards -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916p5007921.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Comparing Charmm 27 energies from GROMACS and NAMD
Actually pdb which is similarly doesn't have velocity information. In this case however I'm mainly interested to see how the potential terms compare between the two packages with Charmm27 ff. Reza On 5/3/13 11:33 AM, Reza wrote: Thanks Mark! No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. The rerun option is interesting - in my case however the potential energy terms stayed identical but the kinetic term became zero. If you are using an .xtc file for the rerun, this makes sense since the .xtc does not store velocities and hence kinetic energy cannot be calculated. -Justin Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. I totally agree :) So far I found out that for no cut-off simulation in Gromacs, rather that specifying a large cut-off, it needs rlist=rvdw=rcoulomb=0 and pbc=no along with ns_type=simple and nstlist=0 (according to the manual). I am running various tests and will update if I find out what is causing the discrepancy. Reza On May 1, 2013, at 5:46 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 1, 2013 at 2:32 PM, Reza Salari resa...@gmail.com wrote: Hi Justin, I actually did :) but it ended up being bigger than 50 kb so it needed moderator approval to show up. I was hoping it would've been released by now. I'll attach a the details below. Any help/hint is highly appreciated. Reza Details: *1)* Both systems were prepared using VMD membrane package and then waters were removed. I used Gromacs 4.6.1 and NAMD 2.9. *2)* Simulations were run in vacuum as a single-point energy calculations (0 step). No, they weren't. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy You cannot hope to reproduce accurately the energy of a configuration if you let the coordinates be manipulated. PME was not used. *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the output was saved as the pdb format. The mdp file: integrator= md nsteps= 0 nstlog = 1 nstlist= 1 ns_type= grid rlist= 100.0 coulombtype= cut-off rcoulomb= 100.0 rvdw= 100.0 pbc = no *4) *NAMD input file: structure ../0_prep/memb_nowat.psf paratypecharmm on parameterspar_all27_prot_lipid.prm exclude scaled1-4 1-4scaling 1.0 switching off switchdist 8 cutoff 1000 pairlistdist 1000 margin 0 timestep 1.0 outputenergies 1 outputtiming 1 binaryoutput no coordinates ../0_prep/memb_nowat.pdb outputname out dcdfreq 10 temperature 300 run 0 *5)* Energies: For Single POPC (kcal/mol) Gromacs NAMD Diff Bond 43.0022 43.0015 -0.0007 Angle 80.6568 80.6571 0.0003 Dih 29.8083 29.8083 0. Imp 0.8452 0.8452 0. Coul -17.2983 -17.2983 0. LJ -7.0798 -7.0798 0. Pot 129.9343 129.9340 -0.0003 The intra-molecule terms look fine. Since this is a lipid, there are non-bonded interactions that are intra-molecule, so the non-bondeds also seem fine. For POPC Memb (kcal/mol) Gromacs NAMD Diff Bond 1539.1181 1539.1162 -0.0019 Angle 3111.9264 3111.9197 -0.0067 Dih 1250.5425 1250.5421 -0.0004 Imp 16.2837 16.2837 0. Coul -1837.8585 -1705.3075 132.5510 LJ -995.0311 -1219.3432 -224.3121 Pot 3084.9904 2993.2110 -91.7794 Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. Mark On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) It appears you hit send too early. Please provide the entirety of the details you intended. Complete .mdp files and actual quantification of the differences you are observing are also very important. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] Re: genion
On 5/3/13 11:52 AM, Ewaru wrote: Hi Justin, Thank you for your prompt reply! My grompp goes like this: grompp -f minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr Is it in the topol.top file? The reason I'm asking this is because I obtained this error while running MD: Yes, you should see 12 ions and 12 fewer water molecules than you had before running genion. If grompp doesn't complain, then your system is neutral. It's a rather simple check. Fatal error: 2 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. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; and thus I was checking if my ions are neutralised or not. There are a whole host of reasons this could be happening. Neutralization is not a likely one. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: genion
Hi Justin, Yup, the grompp works fine. :) Gotta figure out on the Blowing Up now. (.) Thank you once again! Take care. -- View this message in context: http://gromacs.5086.x6.nabble.com/genion-tp5007916p5007924.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] regression tests 4.6.1 with intel 13.0.1
Hi, I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with Intel E5 2600 CPUs After run the regression tests in single precision, I had two failed tests (coulandvdwtogether and vdwalone). Both of them reported this: Different warnings in reference.warn and grompp.warn and the differences are the same ??--[ 12:07:35 ]--\ $ diff reference.warn grompp.warn 6,11d5 With coulomb soft core, the reciprocal space calculation will not necessarily cancel. It may be necessary to decrease the reciprocal space energy, and increase the cutoff radius to get sufficiently close matches to energies with free energy turned off. WARNING 3 [file grompp.mdp]: == In double precision, I had the same failed tests, and one more: simtemp In simtemp checkpot.out has: ??--[ 12:12:36 ]--\ $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 33 terms in the energy files There are 6 terms to compare in the energy files LJ (SR) step 20: 5620.37, step 20: 5609.04 LJ (SR) step 40: 5650.96, step 40: 5628.03 Anglestep 60: 8.55224, step 60: 8.65452 LJ (SR) step 60: 5674.57, step 60: 5643.39 Anglestep 80: 7.04247, step 80: 6.98253 LJ (SR) step 80: 5697.85, step 80: 5658.71 LJ (SR) step 100: 5789.57, step 100: 5748.48 Coulomb (SR) step 100: -31075.7, step 100: -31043.8 Files read successfully Anny suggestions? saludos, José Luis Gordillo Ruiz Coordinación de Supercómputo UNAM -- 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] regression tests 4.6.1 with intel 13.0.1
Were you using the 4.6.1 regression test package? Mark On May 3, 2013 7:53 PM, José Luis Gordillo Ruiz j...@super.unam.mx wrote: Hi, I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with Intel E5 2600 CPUs After run the regression tests in single precision, I had two failed tests (coulandvdwtogether and vdwalone). Both of them reported this: Different warnings in reference.warn and grompp.warn and the differences are the same ??--[ 12:07:35 ]--\ $ diff reference.warn grompp.warn 6,11d5 With coulomb soft core, the reciprocal space calculation will not necessarily cancel. It may be necessary to decrease the reciprocal space energy, and increase the cutoff radius to get sufficiently close matches to energies with free energy turned off. WARNING 3 [file grompp.mdp]: == In double precision, I had the same failed tests, and one more: simtemp In simtemp checkpot.out has: ??--[ 12:12:36 ]--\ $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 33 terms in the energy files There are 6 terms to compare in the energy files LJ (SR) step 20: 5620.37, step 20: 5609.04 LJ (SR) step 40: 5650.96, step 40: 5628.03 Anglestep 60: 8.55224, step 60: 8.65452 LJ (SR) step 60: 5674.57, step 60: 5643.39 Anglestep 80: 7.04247, step 80: 6.98253 LJ (SR) step 80: 5697.85, step 80: 5658.71 LJ (SR) step 100: 5789.57, step 100: 5748.48 Coulomb (SR) step 100: -31075.7, step 100: -31043.8 Files read successfully Anny suggestions? saludos, José Luis Gordillo Ruiz Coordinación de Supercómputo UNAM -- 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] Umbrella sampling's equilibration runs
Couple extra question about umbrella Does it possible to use Collective variable (eigenvector from EDA or NMA) as the pulling coordinate? Does it possible to use output from essential dynamics sampling (here I can use EDS in targeted mode to pull my structure to the target conformation) for the umbrella's NPT+MD. What the input data in the mdp files must be in that case using CV? James 2013/4/30 Justin Lemkul jalem...@vt.edu On 4/30/13 1:38 PM, James Starlight wrote: Justin, could you also tell me 1) what difference should be expected from the umbrella sampling run with (as I want to do for better coverage) and without (as in your tutorial) velocities re-assignment on each umbrella window run ? You have to discard more data at the outset of the production run. Depending on the thermostat, initial forces may cause instability. See previous discussions in the archive on this topic. 2) On what suggestions should I chose each conformer from pulling simulation for each umbrella run? If I have not reasonable kinetiks from the pulling simulation could I chose each conformer based on the RMSD from the starting structure (in some region- eg in active site) assuming that I investigate conformation motions in that region accompanied some functional transitions? The establishment of the reaction coordinates and its component windows depends on what you're examining. I can't tell you that. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] regression tests 4.6.1 with intel 13.0.1
Thank you for pointing out that. I was using regression test 4.6 Now, I tested 4.6.1 regression tests. single precision is fine. Double precision produced two failed tests: vdwalone: ??--[ 13:21:13 ]--\ $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 40 terms in the energy files There are 11 terms to compare in the energy files LJ (SR) step 20: 4318.48, step 20: 4307.68 LJ (SR) step 30: 4320.84, step 30: 4301.83 LJ (SR) step 40: 4340.35, step 40: 4313.65 LJ (SR) step 50: 4371.42, step 50: 4337.92 Coulomb (SR) step 50: -28198.2, step 50: -28169.4 LJ (SR) step 60: 4409.49, step 60: 4369.61 Coulomb (SR) step 60: -28193.8, step 60: -28157.8 Files read successfully ??[ mn324 ]---[ /tmpu/dgsca/jlgr/gromacs-regression-test/regressiontests-4.6.1/freeenergy/vdwalone ] and simtemp = ??--[ 13:23:45 ]--\ $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 33 terms in the energy files There are 6 terms to compare in the energy files LJ (SR) step 20: 5620.37, step 20: 5609.04 LJ (SR) step 40: 5650.96, step 40: 5628.03 Anglestep 60: 8.55224, step 60: 8.65452 LJ (SR) step 60: 5674.57, step 60: 5643.39 Anglestep 80: 7.04247, step 80: 6.98253 LJ (SR) step 80: 5697.85, step 80: 5658.71 LJ (SR) step 100: 5789.57, step 100: 5748.48 Coulomb (SR) step 100: -31075.7, step 100: -31043.8 Files read successfully ??[ mn324 ]---[ /tmpu/dgsca/jlgr/gromacs-regression-test/regressiontests-4.6.1/freeenergy/simtemp ] saludos, José Luis Gordillo Ruiz Coordinación de Supercómputo UNAM El 03/05/2013, a las 13:12, Mark Abraham escribió: Were you using the 4.6.1 regression test package? Mark On May 3, 2013 7:53 PM, José Luis Gordillo Ruiz j...@super.unam.mx wrote: Hi, I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with Intel E5 2600 CPUs After run the regression tests in single precision, I had two failed tests (coulandvdwtogether and vdwalone). Both of them reported this: Different warnings in reference.warn and grompp.warn and the differences are the same ??--[ 12:07:35 ]--\ $ diff reference.warn grompp.warn 6,11d5 With coulomb soft core, the reciprocal space calculation will not necessarily cancel. It may be necessary to decrease the reciprocal space energy, and increase the cutoff radius to get sufficiently close matches to energies with free energy turned off. WARNING 3 [file grompp.mdp]: == In double precision, I had the same failed tests, and one more: simtemp In simtemp checkpot.out has: ??--[ 12:12:36 ]--\ $ more checkpot.out comparing energy file reference_d.edr and ener.edr There are 33 terms in the energy files There are 6 terms to compare in the energy files LJ (SR) step 20: 5620.37, step 20: 5609.04 LJ (SR) step 40: 5650.96, step 40: 5628.03 Anglestep 60: 8.55224, step 60: 8.65452 LJ (SR) step 60: 5674.57, step 60: 5643.39 Anglestep 80: 7.04247, step 80: 6.98253 LJ (SR) step 80: 5697.85, step 80: 5658.71 LJ (SR) step 100: 5789.57, step 100: 5748.48 Coulomb (SR) step 100: -31075.7, step 100: -31043.8 Files read successfully Anny suggestions? saludos, José Luis Gordillo Ruiz Coordinación de Supercómputo UNAM -- 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
Re: [gmx-users] Error after trjconf processing
The problem was solved by adding -pbc mol -ur compact flags to the trjconv. So the problems were indeed in pbc conditions James 2013/5/3 Mark Abraham mark.j.abra...@gmail.com On Fri, May 3, 2013 at 3:17 PM, James Starlight jmsstarli...@gmail.com wrote: Mark, but if I run npt equilibration onto minimized structure (without velocities) without definition of the new velocities in the npt.mdp file gen_vel = No I noticed that in npt.gro file velocities present. Have it been assigned inspite on gen_vel = No in mdp? I can't answer - I don't know from your description and filename what was in 1) the coordinte file you input to the EM grompp, 2) the .gro file you got out of EM mdrun (which presumably went into the NPT grompp), 3) the .tpr file you got out of NPT grompp, and 4) the .gro file you got out of NPT mdrun (which will always have velocities regardless of the foregoing) Please respect your reader's time and describe your observations carefully :-) I think there should never be velocities in 2. Velocities in 3 should follow what the .mdp file said (but if 2 wrote velocities, then it is conceivable that those are still the velocities in 3 iff gen_vel=no, but you would have to inspect the values with gmxdump to see what was happening). Mark -- 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] Potential energy for partial system
Hi all, I been working on a thin film system. To avoid the surface effect, I would like to collect potential energy data for the central region of the thin film by excluding near-surface near-substrate molecules. However, I cannot find any straight forward way to achieve that purpose by using energy group and g_energy. One of my colleagues came up with a recipe to remedy this problem. For me, this recipe makes sense and gives me reasonable quantities. However, I would like to hear comments from the community as well as developers in case I miss something. The recipe outlines as follows. 1. Create an index.ndx that includes a group consisting of all the molecules in the central region. Say the group is called CENTER. 1. Run a MD run for the full system with a energy group CENTER. 2. Use g_energy to obtain the LJ and coulomb interactions between CENTER and the rest system. 3. Use trjconv with index.ndx to create center.trr and center.gro that only contain the trajectory and starting configuration of the central region. 4. Modify the topology file and save as center.top. Specifically, change the number of molecules to just the number of those in the central region. 5. grompp -f mdpfile -c center.top -p center.gro -t center.trr 6. mdrun -rerun center.trr 7. Use g_energy to obtain the potential energy 8. Total potential energy can be acquired by combining the energies from step 3 (intermolecular energy between center and the rest) and step 8( all intramolecular interactions intermolecular interactions among the atoms in center region). Thanks in advance. Po-Han Lin -- 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] Umbrella sampling's equilibration runs
On 5/3/13 2:21 PM, James Starlight wrote: Couple extra question about umbrella Does it possible to use Collective variable (eigenvector from EDA or NMA) as the pulling coordinate? Does it possible to use output from essential dynamics sampling (here I can use EDS in targeted mode to pull my structure to the target conformation) for the umbrella's NPT+MD. What the input data in the mdp files must be in that case using CV? The restraints implemented within the pull code are simply harmonic potentials or rigid constraints along physical vectors. If you want more abstract versions of umbrella sampling, that sounds like a task for something like PLUMED. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] where can be obtain circled lipids bilayer?
Is it really fair to call this a circle? A circle is a 2D object. What you are describing here is a disc. Jesper On May 2, 2013, at 1:13 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: There are indeed circular lipid bilayer structures possible, but they are not found very frequently. See here for example: Seifert, U. Vesicles of toroidal topology. Phys Rev Lett 1991, 66 :2404-2407 Fourcade, B., Mutz, M., Bensimon, D. Experimental and theoretical study of toroidal vesicles. Phys Rev Lett 1992, 68:2551-2554 -- 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] constant protonation state MD
Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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 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] configuration/installation of gromacs-4.6.1 on heterogeneous cluster
Hi, I am struggling with the configuration and compilation/installation of gromacs-4.6.1. Our cluster has 2 different processors: the older generation supports sse4.1, the newer sse4.2. Configuration and compilation must be done on the headnode of the cluster, which supports sse4.2. I am using the following command to configure gromacs-4.6.1: CFLAGS='-fpic -O3 -axSSE4.2,SSE4.1 -xSSSE3 -ip -opt-prefetch' \ CXXFLAGS='-fpic -O3 -axSSE4.2,SSE4.1 -xSSSE3 -ip -opt-prefetch' \ FFLAGS='-fpic -O3 -axSSE4.2,SSE4.1 -xSSSE3 -ip -opt-prefetch' \ CC=mpicc \ CXX=mpicxx \ FC=mpif90 \ LDFLAGS=-lfftw3f -lgoto2 -Wl,-rpath,/usr/local/gromacs-4.6.1/lib \ cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DGMX_MPI=ON \ -DGMX_CPU_ACCELERATION=SSE4.1 -DGMX_OPENMP=OFF -DGMX_GPU=OFF \ -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.1 \ -DCMAKE_SKIP_RPATH=YES \ ../gromacs-4.6.1 However, after compilation/installation mdrun_mpi fails on nodes that only support sse4.1 with Illegal instruction. The CMakeCache.txt file contains the line: BUILD_CPU_FEATURES:INTERNAL=aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 Since this line contains sse4.2 it appears that the flag -DGMX_CPU_ACCELERATION=SSE4.1 is ignored. What is the correct way of specifying the cpu architecture within the cmake build system? (I never had problems with this with the pre 4.6 versions). Cheers, Martin -- Martin Siegert WestGrid/ComputeCanada Simon Fraser University Burnaby, British Columbia Canada -- 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] constant protonation state MD
Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are methods to perform what is called constant-pH MD, where the protonation states of those groups change in a discrete or continuous way along the simulation. If you are interested, start with the corresponding GROMACS how-to (http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and then search the literature. In any case, you don't need any of that fancy stuff unless you have reasons to think that the properties you want to study in your system are strongly dependent on protonation-conformation coupling effects. In some cases you may be suspicious about the effect of the protonation state of one group (e.g., a histidine), but that can be simply tested by performing two constant-protonation MD simulations, one for each state (you can even try to use a linear response approximation on top of that). But in most cases you don't need even that. For what it's worth: I was one of the first to develop and apply constant-pH MD and I don't bother to use it most of the time... :) Best, Antonio On Fri, 3 May 2013, Erik Marklund wrote: Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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 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
[gmx-users] keeping water (entirely) out of the bilayer core
Dear users:
I am interested in running simulations of lipid bilayers in which I keep all
water molecules out of the bilayer core
(not just statistically, but absolutely). However, I have been unable to figure
out how to do it.
I'll list what I have tried in the hope that others have some ideas or even
perhaps know how to do this
with standard gromacs.
Everything that I have tried revolves around using the pull code, setting the
entire lipid bilayer as the reference
group, and having thousands of pulled groups -- one for each water molecule.
Also, I modified the gromacs
source code in mdlib/pull.c (version 4.6.1) so that the force is only applied
when the displacement is smaller than
the desired distance and not when the displacement is larger than the specified
distance (to keep water out but
then to otherwise let it go anywhere without bias):
static void do_pull_pot(int ePull,
t_pull *pull, t_pbc *pbc, double t, real lambda,
real *V, tensor vir, real *dVdl)
{
intg, j, m;
dvec dev;
double ndr, invdr;
real k, dkdl;
t_pullgrp *pgrp;
/* loop over the groups that are being pulled */
*V= 0;
*dVdl = 0;
for (g = 1; g 1+pull-ngrp; g++)
{
pgrp = pull-grp[g];
get_pullgrp_distance(pull, pbc, g, t, pgrp-dr, dev);
/* ## HERE IS THE CODE CHANGE
if(dev[0]0.0){
dev[0]=0.0;
}
/* End code snippit */
The most relevant lines from the .mdp file were:
pull = umbrella
pull_geometry= distance
pull_dim = N N Y
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
... etc...
The problem with this was that it crashed immediately with an error that my
pulling distance was
greater than 1/2 of the box vector.:
Fatal error:
Distance of pull group 165 (5.353939 nm) is larger than 0.49 times the box size
(5.395960)
Pretty obvious in retrospect. If I could get this error to go away, then
everything should be fine because I have modified the code so that forces are
zero at large displacements. However, I am worried that if I simply modify
grompp to bypass this error then I might get some type of strange and possibly
silent error in mdrun. Any thoughts on this are really appreciated.
For my second try, I used pull_geometry = direction-periodic (see more details
below), but that also didn't work
because if I set pull_vec1 = 0 0 1, then everything gets pulled to the upper
part of the box (and LINCS errors
ensue), rather than simply pulling away from the bilayer.
Pcoupl= berendsen
pcoupltype = semiisotropic
compressibility= 4.5e-5 0
pull = umbrella
pull_geometry= direction-periodic
pull_start = no
pull_ngroups = 9000
pull_group0 = POPC
pull_group1 = r_1__OW
pull_init1 = 1.9
pull_k1 = 500
pull_vec1= 0 0 1
pull_group2 = r_2__OW
pull_init2 = 1.9
pull_k2 = 500
pull_vec2= 0 0 1
... etc...
If anybody has an idea about how I could get this to work with standard gromacs
or with a modified version, I would be very grateful to hear your thoughts.
Thank you,
Chris.
--
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Re: [gmx-users] constant protonation state MD
Thanks a lot Erik and Baptista I am interested in simulating the change in secondary structure which is supposed to be influenced by the change in the pH environment of the cell. Experimentally it is not known but it has been proposed by many that the change in pH leads to change in conformation. I did constant protonation state MD at two different pH. I got an alpha helix converting to beta sheet at higher pH but not at lower pH. I am bothered to prove the reliability of the simulation results as experimentally it cant be established. Shahid On Sat, May 4, 2013 at 5:46 AM, bapti...@itqb.unl.pt wrote: Hi Shahid, As Erik said, it depends... on your system, on the process you are studying in that system, on the property you think it's relevant to study that process, etc. If your question refers to the (de)protonation of acidic and basic groups usually occuring in aqueous solution, there are methods to perform what is called constant-pH MD, where the protonation states of those groups change in a discrete or continuous way along the simulation. If you are interested, start with the corresponding GROMACS how-to ( http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulationhttp://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and then search the literature. In any case, you don't need any of that fancy stuff unless you have reasons to think that the properties you want to study in your system are strongly dependent on protonation-conformation coupling effects. In some cases you may be suspicious about the effect of the protonation state of one group (e.g., a histidine), but that can be simply tested by performing two constant-protonation MD simulations, one for each state (you can even try to use a linear response approximation on top of that). But in most cases you don't need even that. For what it's worth: I was one of the first to develop and apply constant-pH MD and I don't bother to use it most of the time... :) Best, Antonio On Fri, 3 May 2013, Erik Marklund wrote: Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends. Erik On 3 May 2013, at 15:27, shahid nayeem msnay...@gmail.com wrote: If I know correctly in lambda dynamics the dynamics of protonation/deprotonation equilibria is accounted for while my question relates to the typical constant protonation MD where each titratable group remains in one protonation state throughout the simulation. Please educate me Shahid On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I don't have one in mind. It's a delicate question and perhaps I shouldn't have phrased it the way I did. Nevertheless, the pKa of most side chains mean that their protonation will be dominated by one state for most pH values. pKa-shifts and complicated interplay between protonation and structure cause exceptions to this and you should be aware that such things may in some cases be important. Also consider the timescales of pH-depedent structural changes and the length of your simulations. You could check out the papers on lambda dynamics by C. Brooks III for an interesting take on sampling multiple protonation states. Best, Erik On 3 May 2013, at 14:05, shahid nayeem msnay...@gmail.com wrote: Thanks a lot Erik. Could I get some reference based on which you say that much of the structural biology will be largely unaffected. Shahid On Fri, May 3, 2013 at 1:05 PM, Erik Marklund er...@xray.bmc.uu.se wrote: There's no general answer to that. Proton conductivity measurements, for instance, will be horribly wrong without dynamic protonation. Much (but not all) structural biology, however, will be largely unaffected. Erik On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote: Dear all Can someone enlighten me on the reliability of the results obtained from constant protonation state (assigned by different pKa value at different pH) MD simulation. Also want to know its reliability in case of implicit solvation model such as PB/GB calculation. Shahid -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)
Sir I am studying protein-ligand interaction through umbrella sampling. I used the following value foe md_pull.mdp file pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = prc pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 and box size details is editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 while runnimg the command for mdrun -s pull.tpr Have the following error Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750) I request you to kindly help me to debug the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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
