Re: [gmx-users] (no subject)
You can probably use gmx solvate for this with the frame at the end of 50 ns as input cp and a box of the new molecules as cs or possibly genion. We also have a tool for building simulation systems with small molecules called DruGUI http://prody.csb.pitt.edu/drugui/ although I don't know how you would convert the topology from NAMD .psf to Gromacs .top format. Best wishes James On Tue, Jul 10, 2018 at 7:21 AM, Soham Sarkar wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and continue it for another 50ns, so > that I can have the effect of that chemicals exclusively before and after > adding it to the system.Is it at all possible? If yes please tell me the > protocol/ commands or give me some references where this type of simulation > is used. Thanks in advance. > -Soham > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Shell (Drude) model for polarization in GROMACS
On 7/15/18 9:14 PM, Eric Smoll wrote: Justin, No problem. That makes sense. Can I send my atp, rtp, itp, and gro files used with the pdb2gmx from your drude branch off-list? Yes, please send a full, self-contained example with any relevant commands or information to reproduce whatever problem you're having. -Justin Best, Eric On Fri, Jul 13, 2018 at 8:12 PM, Justin Lemkul wrote: On 7/13/18 8:14 PM, Eric Smoll wrote: Justin, Your pdb2gmx appears to exclude all intermolecular interactions for a molecule with no hydrogen atoms. For instance, for a molecule with "N" atoms indexed from "1" to "N," the first line of the generated exclusions directive has a record with the "1 2 3...N" series. Is this expected? Shouldn't intramolecular nonbonded interactions be permitted at and beyond 1-4 interactions? I don't want to guess based on files I haven't seen. There's not much I can tell you. -Justin Best, Eric On Fri, Jul 13, 2018 at 3:02 PM, Eric Smoll wrote: Hi Justin, Very grateful for the rapid reply and warning. If you suggest that I should tread lightly with polarizable H atoms, I will avoid it altogether. I will alter my troubleshooting plan and focus on using your edited pdb2gmx program (adding to the rtp, of course) to build a core-shell MD topology for my problem molecules. It should be easy to compare with the topology I have prepared with my own tools. They should be identical. Best, Eric On Fri, Jul 13, 2018 at 2:51 PM, Justin Lemkul wrote: On 7/13/18 4:48 PM, Eric Smoll wrote: Hello Justin, Thank you for the guidance. Although more testing is needed, molecules where shells are attached to every atom appear to be working properly. The issue appears to be with models where shells are only attached to heavy atoms and bonds between hydrogen atoms and heavy atoms are constrained. Initial energy minimization tests (emtol = 100) show that bonds between heavy atoms and hydrogen in organic molecules slowly stretch or compress far more than they should while the network of non-hydrogen atoms maintains a sensible geometry. All atom-drude displacements on the heavy atoms converge quickly and are stable. I am still hunting for whatever topology problem is causing this. All exclusions out to 1-4 interactions between atoms and drudes should be properly included (combined action of the moleculetype directive and additional exclusions directives). Thole screening only applies to atom-shell pairs so no screening is needed for 1-2 and 1-3 pairs with H atoms (no attached shells). It may be difficult to provide any useful guidance without details but troubleshooting suggestions are welcome if you have any. Are there issues associated with adding shells to specific atoms in a molecule? Are simulations that place shells on all atoms (hydrogen and heavy) more stable for some reason? I am going to build a new model where shells are attached to all atoms to see if bonds to hydrogen atoms still slowly compress/stretch during a tight-emtol energy minimization. I have never tested a system like that. Our Drude convention does exactly what you seem to find a problem - Drudes on heavy atoms and not H, with bonds to H constrained. I've never had the issue you're experiencing. Without a full test case of complete inputs, I can't tell you anything. Be forewarned - I know of no efforts by me or anyone else to deal with polarizable H atoms in GROMACS, and that may conflict with constraints, so tread lightly... -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 En
Re: [gmx-users] Shell (Drude) model for polarization in GROMACS
Justin, No problem. That makes sense. Can I send my atp, rtp, itp, and gro files used with the pdb2gmx from your drude branch off-list? Best, Eric On Fri, Jul 13, 2018 at 8:12 PM, Justin Lemkul wrote: > > > On 7/13/18 8:14 PM, Eric Smoll wrote: > >> Justin, >> >> Your pdb2gmx appears to exclude all intermolecular interactions for a >> molecule with no hydrogen atoms. For instance, for a molecule with "N" >> atoms indexed from "1" to "N," the first line of the generated exclusions >> directive has a record with the "1 2 3...N" series. >> >> Is this expected? Shouldn't intramolecular nonbonded interactions be >> permitted at and beyond 1-4 interactions? >> > > I don't want to guess based on files I haven't seen. There's not much I > can tell you. > > -Justin > > > Best, >> Eric >> >> On Fri, Jul 13, 2018 at 3:02 PM, Eric Smoll wrote: >> >> Hi Justin, >>> >>> Very grateful for the rapid reply and warning. If you suggest that I >>> should tread lightly with polarizable H atoms, I will avoid it >>> altogether. >>> >>> I will alter my troubleshooting plan and focus on using your edited >>> pdb2gmx program (adding to the rtp, of course) to build a core-shell MD >>> topology for my problem molecules. It should be easy to compare with the >>> topology I have prepared with my own tools. They should be identical. >>> >>> Best, >>> Eric >>> >>> On Fri, Jul 13, 2018 at 2:51 PM, Justin Lemkul wrote: >>> >>> On 7/13/18 4:48 PM, Eric Smoll wrote: Hello Justin, > > Thank you for the guidance. > > Although more testing is needed, molecules where shells are attached to > every atom appear to be working properly. > > The issue appears to be with models where shells are only attached to > heavy > atoms and bonds between hydrogen atoms and heavy atoms are constrained. > Initial energy minimization tests (emtol = 100) show that bonds between > heavy atoms and hydrogen in organic molecules slowly stretch or > compress > far more than they should while the network of non-hydrogen atoms > maintains > a sensible geometry. All atom-drude displacements on the heavy atoms > converge quickly and are stable. > > I am still hunting for whatever topology problem is causing this. All > exclusions out to 1-4 interactions between atoms and drudes should be > properly included (combined action of the moleculetype directive and > additional exclusions directives). Thole screening only applies to > atom-shell pairs so no screening is needed for 1-2 and 1-3 pairs with H > atoms (no attached shells). It may be difficult to provide any useful > guidance without details but troubleshooting suggestions are welcome if > you > have any. > > Are there issues associated with adding shells to specific atoms in a > molecule? Are simulations that place shells on all atoms (hydrogen and > heavy) more stable for some reason? I am going to build a new model > where > shells are attached to all atoms to see if bonds to hydrogen atoms > still > slowly compress/stretch during a tight-emtol energy minimization. > > I have never tested a system like that. Our Drude convention does exactly what you seem to find a problem - Drudes on heavy atoms and not H, with bonds to H constrained. I've never had the issue you're experiencing. Without a full test case of complete inputs, I can't tell you anything. Be forewarned - I know of no efforts by me or anyone else to deal with polarizable H atoms in GROMACS, and that may conflict with constraints, so tread lightly... -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >>> > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before po
Re: [gmx-users] MDRun Compile issue
I apologilize, it looks like auto-correct hit me again, should be openmpi not openmp From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Weiner, Michael Sent: Sunday, July 15, 2018 3:22 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [EXT] [gmx-users] MDRun Compile issue I am trying to build gromacs 2018.2 on an intel-based HPC that i manage. i have the main program built but i want to build MDrun openmp support. I am using the latest version of Intel Parallel Studio XE (2018.3) in order to compile, as well as the latest boost (1.67.0), gsl (2.5) and openmil (3.1.1) sources. Here is my attemt/configuration to build mdrun with openmpi: - rm -rf * export CC=icc export CXX=icpc export GROMACS_INSTALL_DIR=/cm/shared/apps/gromacs/2018.2 export CMAKE_PREFIX_PATH=/cm/shared/apps/boost/1.67.0:/cm/shared/apps/gsl/2.5 export CFLAGS="-O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp" export CXXFLAGS=$CFLAGS export LDFLAGS=$CFLAGS export MPICC=mpiicc cmake \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_INSTALL_PREFIX=$GROMACS_INSTALL_DIR \ -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_OPENMP=OFF \ -DGMX_EXTERNAL_BLAS=OFF \ -DGMX_BUILD_MDRUN_ONLY=ON \ -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=ON .. && make -j25 mdrun && make install-mdrun -- It gets 95% of the way through the build and fails with the following: [ 93%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o cd /root/temp/gromacs-2018.2/build/src/gromacs && /cm/shared/apps/intel/parallelstudio/2018/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -isystem /root/temp/gromacs-2018.2/src/external/lmfit -I/root/temp/gromacs-2018.2/build/src/contrib/fftw/fftwBuild-prefix/include -I/root/temp/gromacs-2018.2/build/src -isystem /root/temp/gromacs-2018.2/src/external/thread_mpi/include -I/root/temp/gromacs-2018.2/src -isystem /cm/shared/apps/openmpi/gcc/64/3.1.1/include -I/root/temp/gromacs-2018.2/src/external/tng_io/include -I/root/temp/gromacs-2018.2/build/tng/include -mavx -O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp -std=c++11 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -o CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o -c /root/temp/gromacs-2018.2/src/gromacs /mdlib/tpi.cpp /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp(2853): error: identifier "nthreads" is undefined #pragma omp parallel for num_threads(nthreads) schedule(static) ^ compilation aborted for /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp (code 2) make[3]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o] Error 2 Can anyone provide any insights as to why this is failing and perhaps give me some pointers to get it to compile? Thank you Michael Weiner Lead Analyst/UNIX Systems Administrator Lerner Research Institute Computing Services Lerner Research Institute Cleveland Clinic === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff
[gmx-users] MDRun Compile issue
I am trying to build gromacs 2018.2 on an intel-based HPC that i manage. i have the main program built but i want to build MDrun openmp support. I am using the latest version of Intel Parallel Studio XE (2018.3) in order to compile, as well as the latest boost (1.67.0), gsl (2.5) and openmil (3.1.1) sources. Here is my attemt/configuration to build mdrun with openmpi: - rm -rf * export CC=icc export CXX=icpc export GROMACS_INSTALL_DIR=/cm/shared/apps/gromacs/2018.2 export CMAKE_PREFIX_PATH=/cm/shared/apps/boost/1.67.0:/cm/shared/apps/gsl/2.5 export CFLAGS="-O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp" export CXXFLAGS=$CFLAGS export LDFLAGS=$CFLAGS export MPICC=mpiicc cmake \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_INSTALL_PREFIX=$GROMACS_INSTALL_DIR \ -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_OPENMP=OFF \ -DGMX_EXTERNAL_BLAS=OFF \ -DGMX_BUILD_MDRUN_ONLY=ON \ -DGMX_FFT_LIBRARY=fftw3 -DGMX_BUILD_OWN_FFTW=ON .. && make -j25 mdrun && make install-mdrun -- It gets 95% of the way through the build and fails with the following: [ 93%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o cd /root/temp/gromacs-2018.2/build/src/gromacs && /cm/shared/apps/intel/parallelstudio/2018/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -isystem /root/temp/gromacs-2018.2/src/external/lmfit -I/root/temp/gromacs-2018.2/build/src/contrib/fftw/fftwBuild-prefix/include -I/root/temp/gromacs-2018.2/build/src -isystem /root/temp/gromacs-2018.2/src/external/thread_mpi/include -I/root/temp/gromacs-2018.2/src -isystem /cm/shared/apps/openmpi/gcc/64/3.1.1/include -I/root/temp/gromacs-2018.2/src/external/tng_io/include -I/root/temp/gromacs-2018.2/build/tng/include -mavx -O3 -fast-transcendentals -ftz -fma -fp-model fast=2 -qopt-calloc -fp-speculation=fast -fpic -ip -no-prec-div -xHOST -qopenmp -std=c++11 -wd3180 -O3 -DNDEBUG -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -o CMakeFiles/libgromacs.dir/mdlib/tpi.cpp.o -c /root/temp/gromacs-2018.2/src/gromacs /mdlib/tpi.cpp /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp(2853): error: identifier "nthreads" is undefined #pragma omp parallel for num_threads(nthreads) schedule(static) ^ compilation aborted for /root/temp/gromacs-2018.2/src/gromacs/mdlib/nbnxn_search.cpp (code 2) make[3]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o] Error 2 Can anyone provide any insights as to why this is failing and perhaps give me some pointers to get it to compile? Thank you Michael Weiner Lead Analyst/UNIX Systems Administrator Lerner Research Institute Computing Services Lerner Research Institute Cleveland Clinic === Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] [Spam-FG] Re: [Spam-FG] Re: Negative pressure in NVT simulation
If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. Dear Justin, Thanks a lot for your response. Neda - Original Message - From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT) Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation If this email is not spam, click here to submit the signatures to FortiGuard - AntiSpam Service. On 7/15/18 2:32 PM, Neda Rafiee wrote: > ; > energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW > energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW > > freezegrps = SIB OXB OMB SiSil OSil SiGem OGem > freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y You're not using energy group exclusions, which the manual recommends when freezing: "To avoid spurious contributions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time." http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#non-equilibrium-md Freezing is a very severe artificial perturbation, so you will have to use hacks like that if you intend to do a simulation with so many things frozen. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Negative pressure in NVT simulation
On 7/15/18 2:32 PM, Neda Rafiee wrote: ; energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW freezegrps = SIB OXB OMB SiSil OSil SiGem OGem freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y You're not using energy group exclusions, which the manual recommends when freezing: "To avoid spurious contributions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time." http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#non-equilibrium-md Freezing is a very severe artificial perturbation, so you will have to use hacks like that if you intend to do a simulation with so many things frozen. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Negative pressure in NVT simulation
Dear Gromacs users, I have a system part of which is frozen in three dimensions, so I cannot do an NPT. To add solvent to my system, I used solvate but since I am using a user-defined vdwradii.dat to inhibit water enter my solid slab (my slab has a thickness about 3 nm), after some steps I understood that density of water is less than 1000 and so I calculated available volume that water molecules can be added to my box by subtravting the volume of my slab and then I used "gmx insert-molecules" command to add as much water molecules as required to get a density of 1000 Kg/m^3. Now, I am doing NVT and I get correct density for water but I see the pressure in my system is a very large negative number (minus ten to power 24). I want to discuss with you if it is a real problem in my system or not! I am using these mdp options: constraints = none constraint_algorithm = LINCS lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 integrator = md emstep = 0.0001 emtol = 50.0 ; ; Center of mass removal -- comm_mode = none; linear; Change for no pbc comm_grps = system; nstcomm = 10; freq of center of mass removal ; ; Time steps -- dt = 0.001 ;1 fs nsteps = 100 ;1 ns ; ; Output control --- nstxout = 1 ; freq of coord output to trr nstvout = 1 ; freq of velocity output to trr nstfout = 0 ; freq of force output to trr nstlog = 1 ; freq of output to log file nstenergy = 1 ; default of -1 sets equal to nstlist nstxtcout = 1 ; freq of coord output to xtc ; ; Neighbor list and pbc's -- cutoff-scheme = group nstlist = 10; default is 10 -- try more frequent ns_type = grid ; simple (for no pbc) or grid ; pbc = xyz ; CHANGE periodic_molecules = no ; ; Interaction parameters --- rlist = 1 rlistlong = 1 rcoulomb= 1 ; coulombtype = PME epsilon_r = 1 ; vdwtype = user; cut-off rvdw= 1 DispCorr= no ; no or EnerPres ; energygrps = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW freezegrps = SIB OXB OMB SiSil OSil SiGem OGem freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y ; ; temperature coupling is on -- Tcoupl = v-rescale ;or v-rescale berendsen nose-hoover tau_t = 0.3 tc-grps = System ref_t = 300.0 ; Pressure coupling is not on -- Pcoupl = no ; no berendsen Parrinello-Rahman tau_p = 4 pcoupltype = anisotropic ; isotropic anisotropic compressibility = 10.e-5 10.e-5 10.e-5 0.0 0.0 0.0 ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ; distance restraint force constant ;disre = simple ;disre_fc= 1 ; Generate velocites --- gen_vel = yes gen_temp= 300.0 gen_seed= 173529 [ahmadabadi_i.ch.sharif@compute-0-1 1-1_max_ROG_over_Sil]$ cat run.mdp constraints = none constraint_algorithm = LINCS lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 integrator = md emstep = 0.0001 emtol = 50.0 ; ; Center of mass removal -- comm_mode = none; linear; Change for no pbc comm_grps = system; nstcomm = 10; freq of center of mass removal ; ; Time steps -- dt = 0.001 ;1 fs nsteps = 100 ;1 ns ; ; Output control --- nstxout = 1 ; freq of coord output to trr nstvout = 1 ; freq of velocity output to trr nstfout = 0 ; freq of force output to trr nstlog = 1 ; freq of output to log file nstenergy = 1 ; default of -1 sets equal to nstlist nstxtcout = 1 ; freq of coord output to xtc ; ; Neighbor list and pbc's -- cutoff-scheme = group nstlist = 10; default is 10 -- try more
Re: [gmx-users] Convergence of system
I don’t think that autocorrelation is related to convergence of anything. Autocorrelation will tell you how long an interval in a series has to be to extract statistically independent samples of same value. Not clear that has anything to do with convergence, which is the point beyond which you are extracting values from a system that seems to have reached a stable equilibrium. Warren Gallin > On Jul 15, 2018, at 11:46 AM, SHYANTANI MAITI > wrote: > > Dear all, > How to understand whether a system converges from the time correlation > function of the vectors formed by C-alpha? I have constructed the > correlation > function from the eigen vector values of the frames of the trajectory. > After this I have applied the g_analyze function to the xvg file created > from covar function of gromacs. How can I understand the convergence of > system from the correlation function? > > -- > Best regards, > *Shyantani Maiti* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Convergence of system
Dear all, How to understand whether a system converges from the time correlation function of the vectors formed by C-alpha? I have constructed the correlation function from the eigen vector values of the frames of the trajectory. After this I have applied the g_analyze function to the xvg file created from covar function of gromacs. How can I understand the convergence of system from the correlation function? Thanking you -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Convergence of system
Dear all, How to understand whether a system converges from the time correlation function of the vectors formed by C-alpha? I have constructed the correlation function from the eigen vector values of the frames of the trajectory. After this I have applied the g_analyze function to the xvg file created from covar function of gromacs. How can I understand the convergence of system from the correlation function? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/15/18 1:38 AM, farial tavakoli wrote: Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. The problem is still the same: there's nothing called "topolgen.pl" in the working directory. List your files, you'll see it's called something else. Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance . Presumably any of them, but I don't do such calculations. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
