Re: [gmx-users] infinite force at the membrane lipid
Dear Dr Justin and Gromacs User, This is my commands for running energy minimization. define = -DPOSRES integrator = cg nstcgsteep = 1000 emtol = 100.0 emstep = 0.01 dt = 0.002 ; Output control nstxout = 50 nstenergy = 50 nstlog = 50 nstlist = 1 cutoff-scheme = Verlet ns_type = grid coulombtype = PME rcoulomb= 1.2 vdw-modifier= Potential-shift rvdw= 1.2 rvdw-switch = 1.0 pbc = xyz I hope you can give more recommendations. Removing lipids actually is not an appropriate solution. Thank you so much Tuong Vy 2015-08-16 1:47 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 8/15/15 12:41 PM, Vy Phan wrote: Dear All gromacs Users, I want to run the membrane protein simulation. I run the energy minimization for membrane and protein separately. After that I combine protein and lipid together and remove the overlapping molecules. when I run energy minimization I got the error inf at atom on lipid. I remove the lipid which includes this atom. I got the error several time and I repeat remove lipid. I see the inf at atom on lipid always happens on lipids which locate at the wall (at the boundary of unit cell). I successfully run one time when I remove lipids have error, another was failed. I wonder why the error inf at atom on lipid always happens on lipids which locate at the wall. Maybe I did something wrong about periodic boundary condition. Thank you for any thoughts. Without a list of your exact commands and what you've done to this point, it's impossible to diagnose. There's something fundamentally wrong with the coordinates, topology, or both. If the infinite force is just moving around, what you're observing is a symptom, not a cause, and removing lipids to try to make it go away is not an appropriate solution. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] GROMOS atp file
Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what about polar Hydrogens that are bounded to elements other than C (for example H in amino or amid groups)? How should I treat with these polar hydrogens? Kind Regards, Farideh -- 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] reproducibility of trajectory
Hi, I did a 200-ns MD for a protein and found an interesting conformation transition, and according to NMR study in literature, it is believed that 10 us ~ ms scale simulations are needed to get this conformation transition. However, when I tried to reproduce this conformation transition, I was not so lucky any more... I repeated 6 x 200ns trajectories but failed to reproduce, even I used the same seed number. Do you have any ideas on this? Is it sufficient to present this result in papers, since I just got 1 trajectory? Thanks, Qing -- 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] Fwd: [g_mmpbsa] istallation Gromacs 4.6.7 Error
Dear Users i work on gromacs 4.6.1 and ubuntu 14.04 for using* source code* installation for g_mmpbsa, For Gromacs 4.6.7 installation , After using : cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs -DGMX_GPU=off i got this error: CMake Error at cmake/FindFFTW.cmake:122 (message): The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared libraries. Provide a different FFTW library by setting FFTWF_LIBRARY. If you don't have a different one, recompile FFTW with --enable-shared or --with-pic. Or disable shared libraries for Gromacs by setting BUILD_SHARED_LIBS to no. Note: Disabling shared libraries requires up to 10x as much disk space. Call Stack (most recent call first): CMakeLists.txt:923 (find_package) -- Configuring incomplete, errors occurred! See also /home/pdfco/gromacs-4.6.7/build/CMakeFiles/CMakeOutput.log. See also /home/pdfco/gromacs-4.6.7/build/CMakeFiles/CMakeError.log. how can i solve it? i really appriciate for any guid elham -- -- 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] Termini database-more details , meaning of each lines and how to add or delete atoms-reg
how to add and delete atoms and meaning of each lines in both aminoacids.n.tdb and aminoacid.c.tdb My structure is cyclic peptide rings i have to remove Oxygen from -COO end Hydrogen from -NH3 end of the first and last amino acids.. Thank you -- Ragards, Nikhil Maroli -- 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] Termini database-more details , meaning of each lines and how to add or delete atoms-reg
On 8/15/15 1:32 PM, Nikhil Maroli wrote: how to add and delete atoms and meaning of each lines in both aminoacids.n.tdb and aminoacid.c.tdb Read the manual, section 5.6.5 where everything is explained. My structure is cyclic peptide rings i have to remove Oxygen from -COO end Hydrogen from -NH3 end of the first and last amino acids.. This doesn't require .tdb modification. Choose 'None' for the termini and either use specbond.dat to complete the cyclization or manually add the bonded interactions yourself. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] GROMOS atp file
But all the nonbonded parameters for these Hydrogens are zero while they are polar and they should be considered On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 4:42 AM, faride badalkhani wrote: Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what about polar Hydrogens that are bounded to elements other than C (for example H in amino or amid groups)? How should I treat with these polar hydrogens? That's what atom type H is - hydrogen *not* bound to carbon. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Difference in molecule wrapping in gro file
Dear Gromacs users, I just noticed that the gro file written from simulation carried out in Dell cluster and my local desktop workstation have difference in warping the molecules. In server, following grommp and mdrun commands are used, gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.top mpirun -ppn 16 -np 64 gmx_mpi mdrun -deffnm MD5 and the output gro file do not wrap the molecules, i.e I can seen the surface molecules are broken while visualizing the gro file. But, the same simulation using following commands generated the gro file with molecules wrapped well in the box. gmx grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.top gmx mdrun -nt 8 -deffnm MD5 In both case, mdp file have exactly same parameters and the only difference was in nsteps. Can any one help to find out what make this difference in gro file writing? Many thanks Anu -- 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] GROMOS atp file
On 8/15/15 4:42 AM, faride badalkhani wrote: Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what about polar Hydrogens that are bounded to elements other than C (for example H in amino or amid groups)? How should I treat with these polar hydrogens? That's what atom type H is - hydrogen *not* bound to carbon. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] simulation acceleration of SWM4-NDP water and ions
Dear all, I am using polarizable water model (SWM4-NDP) and ions in my simulation. However, the simulation speed is really slow, and it will take several days to get the simulation results. I know the SWM4-NDP only supports 1 MPI thread at the moment. I am wondering if SWM4-NDP supports GPU acceleration, or is there other method to improve the simulation speed? I plan to upgrade my current workstation to speed up the simulation. Any help will be appreciated! Best wishes, Xiaohui SheUniversity of Wisconsin-Madison -- 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] simulation acceleration of SWM4-NDP water and ions
On 8/15/15 9:13 AM, 折晓会 wrote: Dear all, I am using polarizable water model (SWM4-NDP) and ions in my simulation. However, the simulation speed is really slow, and it will take several days to get the simulation results. I know the SWM4-NDP only supports 1 MPI thread at the moment. I am wondering if SWM4-NDP supports GPU acceleration, or is there other method to improve the simulation speed? I plan to upgrade my current workstation to speed up the simulation. Any help will be appreciated! Please see http://dx.doi.org/10.1002/jcc.23937 As a result of that implementation, I also made SCF compatible with domain decomposition, so it is much faster than it was before. The extended Lagrangian is 3x faster than the SCF, but only supports NVT at this point. You can get the force field files and instructions for how to get the code from http://mackerell.umaryland.edu/charmm_drude_ff.shtml There are no tutorials available (lack of time), but for a simple system like water and ions, the example inputs in the SI of the paper are all you should need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] simulation acceleration of SWM4-NDP water and ions
Thank you professor Justin! You are really professional. I will read the documents carefully. Best wishes,Xiaohui Date: Sat, 15 Aug 2015 09:38:38 -0400 From: jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] simulation acceleration of SWM4-NDP water and ions On 8/15/15 9:13 AM, 折晓会 wrote: Dear all, I am using polarizable water model (SWM4-NDP) and ions in my simulation. However, the simulation speed is really slow, and it will take several days to get the simulation results. I know the SWM4-NDP only supports 1 MPI thread at the moment. I am wondering if SWM4-NDP supports GPU acceleration, or is there other method to improve the simulation speed? I plan to upgrade my current workstation to speed up the simulation. Any help will be appreciated! Please see http://dx.doi.org/10.1002/jcc.23937 As a result of that implementation, I also made SCF compatible with domain decomposition, so it is much faster than it was before. The extended Lagrangian is 3x faster than the SCF, but only supports NVT at this point. You can get the force field files and instructions for how to get the code from http://mackerell.umaryland.edu/charmm_drude_ff.shtml There are no tutorials available (lack of time), but for a simple system like water and ions, the example inputs in the SI of the paper are all you should need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] GROMOS atp file
On 8/15/15 9:51 AM, faride badalkhani wrote: But all the nonbonded parameters for these Hydrogens are zero while they are polar and they should be considered This is the convention of the force field. Polar groups are dominated by electrostatics. The van der Waals interactions are parametrized with the assumption that the H do not need LJ terms; the heavy atoms dominate the interaction. This is just the way this particular force field works. Look at the well depth and radii of HC - it's essentially non-existent, as well. -Justin On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 4:42 AM, faride badalkhani wrote: Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what about polar Hydrogens that are bounded to elements other than C (for example H in amino or amid groups)? How should I treat with these polar hydrogens? That's what atom type H is - hydrogen *not* bound to carbon. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] log file not writing simulation time in continuous manner
On 8/15/15 9:51 AM, anu chandra wrote: Dear Gromcas users, I have used grompp, as shown below, to generate .tpr file in order to continue the simulation. gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.top My mdp input parameters are shown below, *** define = -DPOSRES integrator = md dt = 0.002 nsteps = 250 nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT NPROT SOL_ION tau_t = 1.01.0 1.0 ref_t = 303.15 303.15 303.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; gen-vel = no ; nstcomm = 100 comm_mode = linear comm_grps = PROT NPROT SOL_ION ; refcoord_scaling= com *** Unfortunately log file shows simulation time as a new start, not as continuation from previous run, as shown below. Time suppose to start from 10001 ps. ** Started mdrun on rank 0 Sat Aug 15 13:15:04 2015 Step *Time* Lambda 0*0.0 * 0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70981e+041.28824e+059.76982e+042.20959e+032.96128e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.93530e+04 -3.84842e+047.57381e+04 -1.87856e+067.47371e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 1.93759e+030.0e+00 -1.55642e+064.40783e+05 -1.11564e+06 Temperature Pressure (bar) Constr. rmsd 3.03457e+022.41812e+023.91153e-06 DD step 24 load imb.: force 21.2% pme mesh/force 0.689 At step 25 the performance loss due to force load imbalance is 9.0 % NOTE: Turning on dynamic load balancing DD step 999 vol min/aver 0.816 load imb.: force 1.5% pme mesh/force 0.768 Step *Time* Lambda 1000*2.0*0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70890e+041.29741e+059.79287e+042.28826e+032.58526e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.94561e+04 -3.80345e+047.15659e+04 -1.87484e+067.69793e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 2.00424e+030.0e+00 -1.55485e+064.41080e+05 -1.11377e+06 Temperature Pressure (bar) Constr. rmsd 3.03661e+021.71385e+023.91311e-06 * Can any body help me to figure this out? If you continue via grompp, you need to set tinit and init_step to get continuous output. Continuing via the convert-tpr/mdrun -cpi approach will continue seamlessly. If you have provided all of the correct inputs to grompp, the physics is fine; you just need to post-process when concatenating the trajectories (trjcat -settime). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] GROMOS atp file
Thanks a lot for your time and patience. Truly yours, Farideh On Sat, Aug 15, 2015 at 6:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 9:51 AM, faride badalkhani wrote: But all the nonbonded parameters for these Hydrogens are zero while they are polar and they should be considered This is the convention of the force field. Polar groups are dominated by electrostatics. The van der Waals interactions are parametrized with the assumption that the H do not need LJ terms; the heavy atoms dominate the interaction. This is just the way this particular force field works. Look at the well depth and radii of HC - it's essentially non-existent, as well. -Justin On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 4:42 AM, faride badalkhani wrote: Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what about polar Hydrogens that are bounded to elements other than C (for example H in amino or amid groups)? How should I treat with these polar hydrogens? That's what atom type H is - hydrogen *not* bound to carbon. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] log file not writing simulation time in continuous manner
Dear Justin, Thanks a lot for your prompt reply. On Sat, Aug 15, 2015 at 2:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 9:51 AM, anu chandra wrote: Dear Gromcas users, I have used grompp, as shown below, to generate .tpr file in order to continue the simulation. gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n index.ndx -p topol.top My mdp input parameters are shown below, *** define = -DPOSRES integrator = md dt = 0.002 nsteps = 250 nstlog = 1000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb= 1.2 vdwtype = Cut-off vdw-modifier= Force-switch rvdw_switch = 1.0 rvdw= 1.2 ; tcoupl = Nose-Hoover tc_grps = PROT NPROT SOL_ION tau_t = 1.01.0 1.0 ref_t = 303.15 303.15 303.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm= LINCS continuation= yes ; gen-vel = no ; nstcomm = 100 comm_mode = linear comm_grps = PROT NPROT SOL_ION ; refcoord_scaling= com *** Unfortunately log file shows simulation time as a new start, not as continuation from previous run, as shown below. Time suppose to start from 10001 ps. ** Started mdrun on rank 0 Sat Aug 15 13:15:04 2015 Step *Time* Lambda 0*0.0 * 0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70981e+041.28824e+059.76982e+042.20959e+03 2.96128e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.93530e+04 -3.84842e+047.57381e+04 -1.87856e+06 7.47371e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 1.93759e+030.0e+00 -1.55642e+064.40783e+05 -1.11564e+06 Temperature Pressure (bar) Constr. rmsd 3.03457e+022.41812e+023.91153e-06 DD step 24 load imb.: force 21.2% pme mesh/force 0.689 At step 25 the performance loss due to force load imbalance is 9.0 % NOTE: Turning on dynamic load balancing DD step 999 vol min/aver 0.816 load imb.: force 1.5% pme mesh/force 0.768 Step *Time* Lambda 1000*2.0*0.0 Energies (kJ/mol) BondU-BProper Dih. Improper Dih. CMAP Dih. 2.70890e+041.29741e+059.79287e+042.28826e+03 2.58526e+02 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. 1.94561e+04 -3.80345e+047.15659e+04 -1.87484e+06 7.69793e+03 Position Rest. Dih. Rest. PotentialKinetic En. Total Energy 2.00424e+030.0e+00 -1.55485e+064.41080e+05 -1.11377e+06 Temperature Pressure (bar) Constr. rmsd 3.03661e+021.71385e+023.91311e-06 * Can any body help me to figure this out? If you continue via grompp, you need to set tinit and init_step to get continuous output. Continuing via the convert-tpr/mdrun -cpi approach will continue seamlessly. If you have provided all of the correct inputs to grompp, the physics is fine; you just need to post-process when concatenating the trajectories (trjcat -settime). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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
Re: [gmx-users] infinite force at the membrane lipid
On 8/15/15 12:41 PM, Vy Phan wrote: Dear All gromacs Users, I want to run the membrane protein simulation. I run the energy minimization for membrane and protein separately. After that I combine protein and lipid together and remove the overlapping molecules. when I run energy minimization I got the error inf at atom on lipid. I remove the lipid which includes this atom. I got the error several time and I repeat remove lipid. I see the inf at atom on lipid always happens on lipids which locate at the wall (at the boundary of unit cell). I successfully run one time when I remove lipids have error, another was failed. I wonder why the error inf at atom on lipid always happens on lipids which locate at the wall. Maybe I did something wrong about periodic boundary condition. Thank you for any thoughts. Without a list of your exact commands and what you've done to this point, it's impossible to diagnose. There's something fundamentally wrong with the coordinates, topology, or both. If the infinite force is just moving around, what you're observing is a symptom, not a cause, and removing lipids to try to make it go away is not an appropriate solution. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
