[gmx-users] Problem with OPLS parameters (too few parameters on line)
Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I followed the chris neale directives to make the necessary changes i.e. sigma and epsilon, I incorporated the modified atom types of lipids in oplsaanb_lipid.itp LOLO115.99940A0.29530.87869434 ;carbonyl O, OPLS" LOMLOM115.99940A0.29530.87869434 ;carboxyl O, OPLS I also made changes to the [pair types] and appended them in the oplsaanb_lipid.itp file [ pair types ] ; ijfuncsigmaepsilon LOLO10.296037630.10964147 LOLOM10.296037630.10964147 LOopls_11610.3063169020.094663158 and also changed the OW to opls_116 and removed HW lines. Now I want to generate the tpr file using grompp where I had generated a topol_popc.top : -- ; Include chain topologies #include "oplsaa_lipid.ff/forcefield.itp" #include "popc.itp" ; Include water topology #include "oplsaa_lipid.ff/spc.itp" ; System specifications [ system ] 128-Lipid POPC Bilayer [ molecules ] ; molecule name nr. POPC 128 SOL 2460 - Now when I run the grompp command it gives me following error: ERROR 1 [file ffoplsaanb_lipid.itp, line 852]: Invalid directive pair types WARNING 1 [file ffoplsaanb_lipid.itp, line 854]: Too few parameters on line (source file toppush.c, line 246) - Generated 359128 of the 359128 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 359128 of the 359128 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'POPC' There were 91 warnings --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1372 Fatal error: There was 1 error in input file(s) I am not able to get where I am going wrong. Thanking you, Parul -- 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] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation
Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I wanted to modify the parameter files of lipids taken from peter teilman site. Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6 and c12 to sigma epsilon using formula Sigma = (c12/c6)^1/6 and epsilon = c6/(4*sigma^6) i tried it for the [pairtypes] in lipid.itp file, but the calculations I made using excel gave me the following: [ pairtypes ] ; i j funct sigma epsilon LO LO 1 1.10E-012.96E-01 LO LOM 1 1.10E-012.96E-0 and so on i.e. the values of sigma and epsilon are interchanged, as opposed to the values listed by chris neale in archive mail (listed below) [ pairtypes ] ; i j funct sigma epsilon LO LO 1 2.96E-011.10E-01 LO LOM 1 2.96E-011.10E-01 LO opls_1161 3.06E-019.47E-02 LO LNL 1 3.10E-019.88E-02 LO LC 1 3.33E-017.76E-02 etc... I am doing something wrong or I can just interchange the values and use them accordingly. Thanking you Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with generating topology file for OPLS force field for membrane protein simulation
Dear GMX users, I am working on a protein which I want to simulate in a lipid bilayer environment (POPC) and want to use OPLS force field for the same. I have previously rum the membrane protein simulations using 43a6 force field with the help of justin's tutorial which had run quite fine. But I am having problems for generating a topology file for OPLS ff to incorporate both lipid and protein's topology. As the OPLS ff only contains atomtypes in ffoplsaanb.itp file only contains the atom types, I am not able to make out what necessary changes to follow to generate a topology file incorporating both lipid and protein. lso the POPC lipid.itp (acquired from university of calgary website) is quite different from the default ffoplsaanb file so I was wondering if there is source to get the OPLS force field parameters for lipids. Thanking you, Parul Tewatia -- 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 problem of gromacs 4.0.7 on Rocks cluster
Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi we got the following error: 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 for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc 2. command ./configure --enable-float --enable-threads --enable-sse --enable-mpi --program-suffix=_mpi MPICC="/usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx" we got the following error: 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 for mpxlc... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx checking whether the MPI cc command works... yes checking for catamount... no checking for pthreads... yes checking how to run the C preprocessor... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx -E checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -funroll-all-loops... yes checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no 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 whether byte ordering is bigendian... no checking for int... yes checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. though the installation completes without the --enable mpi the gcc compiler version used is 4.1.2. i will be grateful if someone can help us out on how to resolve this issue. thanking you, Parul Tewatia -- 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: gmx-users Digest, Vol 89, Issue 107
Thanks for the reply Justin, > > In theory, that should work. Please post the entirety of your .mdp file. > > Have you done any prior equilibration, or have you moved straight into > annealing? I would suggest a restrained NVT before applying NPT or > annealing > when using the restraints. > Yes I did the restrained NVT before but the same problem came, morover there was a hole in the upper part of the system with the SOL molecules displaced. So then I tried to run the annealing but in this case the SOL molecules were intact but similar problem came with the lipid membrane. though, just to check then I tried to equilibration with restrained NVT where I restrained the movement of the lipid in all the x, y, z axis the problem did not occur. Here is my mdp file -- title = NVT equilibration for B3-DPPC define= -DPOSRES -DPOSRES_LIPID ; position restrain the protein and lipid ; Run parameters integrator = md; leap-frog integrator nsteps= 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog= 100 ; update log file every 0.2 ps ; Bond parameters continuation = no; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 323 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- -- This is the topology file: -- ;Include DPPC chain topology #include "dppc.itp" #ifdef POSRES_LIPID ; Position restraint for each lipid #include "lipid_posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound #mols Protein_A 1 DPPC 121 SOL 9867 CL- 14 -- thanks Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with lipid membrane
Thanks for the reply Justin, This is how I added the position restraint in topology -- ; Include DPPC chain topology #include "dppc.itp" #ifdef POSRES_LIPID ; Position restraint for each lipid #include "lipid_posre.itp" #endif -- And this is how the define statement is in .mdp file -- title = Simulated Annealing for B3-DPPC define = -DPOSRES -DPOSRES_LIPID ; restrain protein and lipid P8 -- Maybe there is some problem I am not able to figure. Thanks. Parul Parul tew wrote: > Dear Gmx users, > > > > I am working on a transmembrane protein and my system contains protein, DPPC > > bilayer, water (spc) and ions. After adding ions I energy minimized the > system and used trjconv to remove periodicity. In the equilibration It is unnecessary to manipulate the output file at this stage. Be sure you're not doing anything funny to the coordinates that cause the problem described below. > phase the lipid molecules were entering the voids in the solvent leaving > the protein naked. So, I used position restraint on the Z-plane and > restrained the phosphate head (atom 8) and one carbon atom on each tail > (atoms 31, 50 with a force constant of 1,000 kJ mol/−/1 nm/−/2. > > --- > > ; position restraint file for DPPC > > > > [ position_restraints ] > > ; i funct fcxfcyfcz > >81 0 0 1000 > > 311 0 0 1000 > > 501 0 0 1000 > > > > --- > > But after running a simulated annealing for 500ps I get a distorted > lipid membrane where the lipids tend to pack at one end but open at the > other end of the box. > > After this I had put position restraint on all the atoms of the lipid on > the z-plane and again tried the simulated annealing but it gave the same > result. > > I am not able to understand where I am going wrong. > The fact that none of the approaches is working suggests to me that either the topology does not #include the position restraint file or you do not have the proper "define" statement in your .mdp file. A simple restraint on P8 in the Z-dimension should prevent distortions; I use such a technique routinely. -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] problem with lipid membrane
Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After adding ions I energy minimized the system and used trjconv to remove periodicity. In the equilibration phase the lipid molecules were entering the voids in the solvent leaving the protein naked. So, I used position restraint on the Z-plane and restrained the phosphate head (atom 8) and one carbon atom on each tail (atoms 31, 50 with a force constant of 1,000 kJ mol*-*1 nm*-*2. --- ; position restraint file for DPPC [ position_restraints ] ; i funct fcxfcyfcz 81 0 0 1000 311 0 0 1000 501 0 0 1000 --- But after running a simulated annealing for 500ps I get a distorted lipid membrane where the lipids tend to pack at one end but open at the other end of the box. After this I had put position restraint on all the atoms of the lipid on the z-plane and again tried the simulated annealing but it gave the same result. I am not able to understand where I am going wrong. Thanks, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem of lipid molecules entering voids of solvent during equilibration
Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of 100ps, the lipid molecules enter the voids in the solvent leaving the protein naked. I have already used position restraint at the inflate.gro steps, now I have read that I can use the option to freeze the groups which I can do at the z axis to avoid the lipid headgroups to enter the void of the solvent. The manual suggests starting with freezing in a constant volume simulation and afterwards using position restraints in conjunction with constant pressure. Now, Is it feasible if I freeze the lipids in z-axis for the whole course of simulation or should I do it only during the equilibration phase? Is there any alternative which I can use during simulation to avoid this? My nvt.mdp is: --- title = NVT equilibration for B3-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps= 5 ; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order= 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2; short-range neighborlist cutoff (in nm) rcoulomb = 1.2; short-range electrostatic cutoff (in nm) rvdw = 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.10.1 0.1 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm= 1 comm-mode = Linear comm-grps= Protein_DPPC SOL_CL- thanks, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: problem during Energy minimization
gmx-users@gromacs.org Dear Gmx users, I am working on a transmembrane protein and my system contains protein, DPPC bilayer, water (spc) and ions. After preparing my system for simulation I have successfully performed the energy minimization, I am facing a problem at the nvt equilibration phase of 100ps, the lipid molecules enter the voids in the solvent leaving the protein naked. I have already used position restraint at the inflate.gro steps, now I have read that I can use the option to freeze the groups which I can do at the z axis to avoid the lipid headgroups to enter the void of the solvent. The manual suggests starting with freezing in a constant volume simulation and afterwards using position restraints in conjunction with constant pressure. Now, Is it feasible if I freeze the lipids in z-axis for the whole course of simulation or should I do it only during the equilibration phase? Is there any alternative which I can use during simulation to avoid this? My nvt.mdp is: --- title = NVT equilibration for B3-DPPC define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps= 5 ; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order= 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2; short-range neighborlist cutoff (in nm) rcoulomb = 1.2; short-range electrostatic cutoff (in nm) rvdw = 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale; modified Berendsen thermostat tc-grps = Protein DPPC SOL_CL- ; three coupling groups - more accurate tau_t = 0.10.1 0.1 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm= 1 comm-mode = Linear comm-grps= Protein_DPPC SOL_CL- thanks, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem during Energy minimization
Dear GMX users, I am facing problem while doing energy minimization before the molecular dynamic simulation step of a system consisting of protein, membrane, water and 14 ions. The minim.mdp file is as follows - ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist = 1.2; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions * - * when I run this using the command * * *grompp –f minim.mdp –c system_sol_ions.gro -p topol.top –o em.tpr * then I invoked mdrun which gave following error Reading file topol.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force =inf on atom 1417 Norm of force =inf - After this I changed the emstep = 0.1 ; Energy step size nsteps = 5000 ; Maximum number of (minimization) steps to perform constraints = none After these changes the no of steps increased to 18 but still the system did not converge and potential energy is very high -- Reading file em.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 5000 Step= 17, Dmax= 1.5e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force =inf on atom 1417 Norm of force =inf What changes can I do in my minim.mdp file to converge my system and get a negative value of Epot. The topol.top file looks -- [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound#mols Protein_A 1 DPPC121 SOL 11107 CL- 14 - Thanks, Parul -- 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-
[gmx-users] problem during energy minimization before MD
Dear GMX users, I am facing problem while doing energy minimization before the molecular dynamic simulation step of a system consisting of protein, membrane, water and 14 ions. The minim.mdp file is as follows - ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist = 1.2; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions * - * when I run this using the command * * *grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em.tpr * then I invoked mdrun which gave following error Reading file topol.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force =inf on atom 1417 Norm of force =inf - After this I changed the emstep = 0.1 ; Energy step size nsteps = 5000 ; Maximum number of (minimization) steps to perform constraints = none After these changes the no of steps increased to 18 but still the system did not converge and potential energy is very high -- Reading file em.tpr, VERSION 4.0.7 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 5000 Step= 17, Dmax= 1.5e-06 nm, Epot= 3.03531e+22 Fmax= inf, atom= 1417 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 18 steps, but did not reach the requested Fmax < 1000. Potential Energy = 3.0353124e+22 Maximum force =inf on atom 1417 Norm of force =inf What changes can I do in my minim.mdp file to converge my system and get a negative value of Epot. The topol.top file looks -- [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound#mols Protein_A 1 DPPC121 SOL 11107 CL- 14 - Thanks, Parul -- 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-r
[gmx-users] problem in energy minimization of the inflted system
Dear GMX users, I am facing problem while doing energy minimization of the inflated system of a protein with membrane. I inflated the system and updated the removed lipids in the topology file. Now I am stuck during the energy minimization state. Below is the .mdp file for minimization. - ; minim_1.mdp - used as input into grompp to generate em_1.tpr integrator = cg; Algorithm (cg = conjugate gradient minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off gen_vel = yes define = DSTRONG_POSRES when I run this using the command *grompp –f minim_1.mdp –c system_inflated.gro topol.top –o em_1.tpr * it generates the em_1.tpr file but does not generate any md_out.mdp file and it gives the following 2 notes Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# checking input for internal consistency... processing topology... *NOTE 1 [file topol.top, line 24414]:* ** System has non-zero total charge: 1.42e+01 processing coordinates... double-checking input for internal consistency... Reading position restraint coords from system_inflated.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/Gromacs/share/top/aminoacids.dat There are: 121 OTHER residues There are: 408PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 9931 elements Making dummy/rest group for Acceleration containing 9931 elements Making dummy/rest group for Freeze containing 9931 elements Making dummy/rest group for Energy Mon. containing 9931 elements Making dummy/rest group for VCM containing 9931 elements Number of degrees of freedom in T-Coupling group rest is 29790.00 Making dummy/rest group for User1 containing 9931 elements Making dummy/rest group for User2 containing 9931 elements Making dummy/rest group for XTC containing 9931 elements Making dummy/rest group for Or. Res. Fit containing 9931 elements Making dummy/rest group for QMMM containing 9931 elements Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x55, spacing 0.119 0.119 0.120 Estimate for the relative computational load of the PME mesh part: 0.96 *NOTE 2 [file aminoacids.dat, line 1]:* ** The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing This run will generate roughly 116 Mb of data writing run input file... There were 2 notes gcq#22: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black) --I understand the note 1 as I haven’t added the ions yet, so the system has charge. But I am confused about note 2, what changes can I make to .mdp file for the minimization to run smoothly. Thanks, Parul -- 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] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
Hi all, first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me. I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the inflategro.pl script and and now I am facing a problem doing energy minimization of my inflated system (contatining protein and the lipid membrane) using grompp. I have updated my topology file accordingly ie removed the spc.itp, ions.itp it now only contains protein and dppc the protein is of 3881 atoms but after updating my topolgy it still gives the following error: Fatal error: number of coordinates in coordinate file (system_inflated.gro, 9331) does not match topology (topol.top, 10281) As i understand it could be because of the deleted lipids of the system, if so how can I know the deleted number of lipids. My topology file looks like - ; ; This is your topology file ; protein ; ; Include forcefield parameters #include "ffG53a6_lipid.itp" [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] . . . . ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include DPPC chain topology #include "dppc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name protein 128-Lipid DPPC Bilayer [ molecules ] ; Compound#mols Protein_A 1 DPPC128 thank you, Parul Tewatia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to define the box when protein protruding out of the lipid bi layer membrane
the protein I am working on is a very large transmembrane protein. I used the DPPC bi layer membrane from peter teilman site and moved my protein into the membrane using VMD. the protein being very big is protruding out of the lipid membrane. Now I want to solvate my whole protein for simulation studies. I am following the Justin A lemkul tutorial KALP15 in DPPC in step 3 we have to define the dimensions of the box to solvate the whole system. what could be the How can I define the box so that my whole protein is inside the box. In the tutorial as I understand in the editconf step we have to give the membrane box vectors but if i will do so my protein will be out of the box. That is to say I want to fill spc (water ) above and below the bilayer DPPC so that I have a fully solvated system. 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] Atomtype HW not found when using grompp for energy minimization
Hello, I get the following error when I try to run grompp cpmmand for energy minimization in GROMACS of DPPC membrane ... checking input for internal consistency... processing topology... --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 843 Fatal error: Atomtype HW not found the topology file of the DPPC contains: -- ; This is your topology file ; 1SOL OW1 -2.449 -4.190 -1.80 ; ; Include chain topologies #include "ffG53a6_lipid.itp" #include "dppc.itp" ; Include water topology ;include "spc.itp" ; Include ion topologies ;include "ions.itp" ; System specifications [ system ] 128-Lipid DPPC Bilayer [ molecules ] ; molecule name nr. DPPC 128 SOL 3655 I am using ffG53a6 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
