[gmx-users] Signal: Segmentation faul
hi, HAPPY NEW YEAR I am experiencing a segmentation fault during mdrun in equlibration step . error Wrote pdb files with previous and current coordinates [shikha-desktop:01719] *** Process received signal *** [shikha-desktop:01719] Signal: Segmentation fault (11) [shikha-desktop:01719] Signal code: Address not mapped (1) [shikha-desktop:01719] Failing at address: 0x8d22a70 [shikha-desktop:01719] [ 0] [0xb87410] [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789] [shikha-desktop:01719] *** End of error message *** Segmentation fault bottom lines of my .log file after energy minimization is this Step Time Lambda 1135711357.00.0 Step Time Lambda 1135811358.00.0 Step Time Lambda 1135911359.00.0 Step Time Lambda 1136011360.00.0 Step Time Lambda 1136111361.00.0 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) Steepest Descents converged to machine precision in 11362 steps, but did not reach the requested Fmax < 1000. Potential Energy = -5.4871900e+06 Maximum force = 3.9830833e+03 on atom 4511 Norm of force = 1.9521437e+01 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - LJ 10523.695513 347281.952 0.4 Coul(T) 6405.625131 269036.256 0.3 Coul(T) [W3] 226.446553 28305.819 0.0 Coul(T) + LJ 4637.739866 255075.693 0.3 Coul(T) + LJ [W3] 1706.661036 235519.223 0.3 Coul(T) + LJ [W3-W3]141595.84421154089612.48969.1 Outer nonbonded loop 18947.604080 189476.041 0.2 1,4 nonbonded interactions 105.1893969467.046 0.0 Calc Weights 11755.000218 423180.008 0.5 Spread Q Bspline250773.337984 501546.676 0.6 Gather F Bspline250773.337984 1504640.028 1.9 3D-FFT 1217431.505524 9739452.04412.4 Solve PME14842.953216 949949.006 1.2 NS-Pairs418574.562328 8790065.80911.2 Reset In Box 1338.8867184016.660 0.0 Shift-X 3916.765450 23500.593 0.0 CG-CoM3918.333406 11755.000 0.0 Bonds 114.1312906733.746 0.0 Angles 142.695358 23972.820 0.0 Propers102.167104 23396.267 0.0 Impropers 28.9844626028.768 0.0 RB-Dihedrals 2.885948 712.829 0.0 Pos. Restr. 38.1990441909.952 0.0 Virial3918.844696 70539.205 0.1 Settle2534.725856 818716.451 1.0 - Total78323890.379 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Neighbor search1 1136230337.457 6067.718.8 Force 1 1136235859.263 7172.122.3 PME mesh 1 1136212486.060 2497.3 7.8 Constraints1 22723 1294.000 258.8 0.8 Rest 1 81096.73016219.850.3 --- Total 1 161073.51132215.7 100.0 --- --- PME spread/gather 1 22724 7169.616 1434.0 4.5 PME 3D-FFT 1
[gmx-users] Potential Energy = -nan
hi, I tried on other system , 4GB ram , core i3 ,64bit processor ; 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= 10.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; 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= Shift; 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 (yes/no) nstxout = 1 result Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=25000 Step= 14, Dmax= 1.2e-06 nm, Epot= -nan Fmax= 3.56233e+07, atom= 2455 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up after_em2.gro to ./#after_em2.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! shikha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Potential Energy = -nan
hi, I m tried nstxout=1 in my .mdp file. Potential Energy = -nan Maximum force = 3.5637456e+07 on atom 2455 Norm of force = -nan help me! regards: shikha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Potential Energy = -nan
hi > > I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . Intel 32. I can perform simple task . I m trying nstxout=1 in my .mdp file. I will report u later. What is the hardware type? PowerPC, Intel 32- or 64-bit, etc? > when i skiped scaling by factor 0.95 then , after EM step I m getting > same potential energy nan result. > Do other simple systems work? Can you do simple tutorial systems like lysozyme in water? Otherwise, you've got some topology problem that prevents the system from being properly minimized. Set nstxout=1 in your .mdp file and watch what's happening. -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] Potential Energy = -nan
hi > I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk . when i skiped scaling by factor 0.95 then , after EM step I m getting same potential energy nan result. > i m doing simulation membrane protein > while scaling down the lipids by a factor of 0.95 then performing EM > > Steepest Descents converged to Fmax < 10 in 18 steps > Potential Energy = -nan > Maximum force = 4.7791553e+02 on atom 5440 > Norm of force = -nan > > > > ; 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= 10.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.1 ; Energy step size > nsteps= 25000 ; Maximum number of (minimization) steps > to perform > > ; Parameters describing how to find the neighbors of each atom and how > to calculate the interactions > nstlist= 10; 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= Shift; 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 (yes/no) > define = -DSTRONG_POSRES > > > earlier when i was using > > ; 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 (yes/no) > define = -DFLEXIBLE > > > then problem was same > Which version of Gromacs? On what hardware? I discovered a platform-specific bug that looked a lot like this, but I hesitate to suggest that until I know more. In all likelihood, you simply have unresolvable atomic overlap (i.e., you're packing too much) such that energy minimization cannot complete, since nan = "not a number," or something is infinitely large or small. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Potential Energy = -nan
hi i m doing simulation membrane protein while scaling down the lipids by a factor of 0.95 then performing EM Steepest Descents converged to Fmax < 10 in 18 steps Potential Energy = -nan Maximum force = 4.7791553e+02 on atom 5440 Norm of force = -nan ; 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= 10.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.1 ; Energy step size nsteps= 25000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 10; 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= Shift; 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 (yes/no) define = -DSTRONG_POSRES earlier when i was using ; 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 (yes/no) define = -DFLEXIBLE then problem was same help me ! with regards: shikha -- 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] No such moleculetype NA+
hello , this is my ions.itp file for gromos53a6 forcefield [ moleculetype ] ; molnamenrexcl CU11 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU1+1CU1CU 11 63.54600 [ moleculetype ] ; molnamenrexcl CU1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU2+1CUCU 12 63.54600 [ moleculetype ] ; molnamenrexcl ZN1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1ZN2+1ZNZN 12 65.37000 this is my ions.itp [ moleculetype ] ; molnamenrexcl MG1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1MG2+1MGMG 12 24.30500 [ moleculetype ] ; molnamenrexcl CA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CA2+1CACA 12 40.08000 [ moleculetype ] ; molnamenrexcl NA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1NA+1NANA 11 22.9898 [ moleculetype ] ; molnamenrexcl CL1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CL-1CLCL 1-1 35.45300 for adding ions I used this command ... genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 -nname CL- now when I m doing EM then getting this error grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr Fatal error: No such moleculetype NA+ help me ! regards: shikha -- 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] generate .top file
hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include "forcefield.itp" #include "pope.itp" ; Include water topology #include "spc.itp" ; Include ion topologies #include "ions.itp" ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 but it should contain protein molecule .what should be topology file ,, how to generate that for system.gro according to tutorial. my protein has 344 molecules . I tried to use g_x2top but it is not available for gromos53a6. help! thank for ur support ! with regards : shikha -- 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 does not match topology
hello I m unable to update the [ molecules ] directive of topol_pope.top . grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr Fatal error: number of coordinates in coordinate file (system_inflated.gro, 20782) does not match topology (topol_pope.top, 37867) this is my .top file ; Include chain topologies #include "forcefield.itp" #include "pope.itp" ; Include water topology #include "spc.itp" ; Include ion topologies #include "ions.itp" ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 this is system.gro Gnomes, ROck Monsters And Chili Sauce 41229 this is sytem_inflated.gro What you read here has nothing to do with anything. So you don't have to read it. Thank you. 20782 but there is 3362 protein atom and 17680 lipid in sytem_inflated.gro then why inflategro.pl script is generating wrong total count . help! thank for ur support ! with regards : shikha -- 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] reading tpx file version 73 with version 58 program
hi , Mr. justin thanx a lot for ur help! now i m able to generate system_inflated.gro. but while i m performing Run energy minimization accorning to tutorial getting this error grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em1.tpr mdrun -v -s em1 -o em1 -c after_em -g emlog Fatal error: reading tpx file (em1.tpr) version 73 with version 58 program with regards: shikha IIIT-A -- 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] Illegal division by zero at inflategro
Hi I am having a trouble during inflategro scaling my system.gro perl inflategro system.gro 4 POPE 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro line 300. regards: shikha -- 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] Unknown bond_atomtype MNH3
Hello Justin, Thank you for your reply. I modifed ffG53a6bn_lipid.itp [ atomtypes ] ;name mass charge ptype c6 c12 ; LO15.99940.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM15.99940.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL14.00670.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS LC12.01100.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS LH113.01900.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS LH214.02700.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS LP30.97380.000 A 9.16000e-03 2.50700e-05 ;phosphor, OPLS LOS15.99940.000 A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS LP214.02700.000 A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ LP315.03500.000 A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ LC315.03500.000 A 9.35700e-03 3.60900e-05 ;CH3, OPLS LC214.02700.000 A 5.94700e-03 1.79000e-05 ;CH2, OPLS OW0.000 0.000 A 2.617345-03 2.63412e-06 [ nonbond_params ] ; ijfuncc6 c12 LOLO 1 2.36400e-03 1.59000e-06 LO LOM 1 2.36400e-03 1.59000e-06 LO LNL 1 2.81600e-03 2.50600e-06 LOLC 1 3.39900e-03 4.64800e-06 LO LH1 1 3.08700e-03 4.39300e-06 LO LH2 1 4.06900e-03 6.28300e-06 LOLP 1 4.65300e-03 6.31300e-06 LO LOS 1 2.46100e-03 1.72300e-06 LO LP2 1 3.72700e-03 6.0e-06 LO LP3 1 4.55500e-03 7.33500e-06 LO LC3 1 4.70300e-03 7.57400e-06 LO LC2 1 3.74900e-03 5.33500e-06 LOM LOM 1 2.36400e-03 1.59000e-06 LOM LNL 1 2.81600e-03 2.50600e-06 LOMLC 1 3.39900e-03 4.64800e-06 LOM LH1 1 3.08700e-03 4.39300e-06 LOM LH2 1 4.06900e-03 6.28300e-06 LOMLP 1 4.65300e-03 6.31300e-06 LOM LOS 1 2.46100e-03 1.72300e-06 LOM LP2 1 3.72700e-03 6.0e-06 LOM LP3 1 4.55500e-03 7.33500e-06 LOM LC3 1 4.70300e-03 7.57400e-06 LOM LC2 1 3.74900e-03 5.33500e-06 LNL LNL 1 3.35300e-03 3.95100e-06 LNLLC 1 4.04900e-03 7.32800e-06 LNL LH1 1 3.67700e-03 6.92500e-06 LNL LH2 1 4.84600e-03 9.90500e-06 LNLLP 1 5.54200e-03 9.95300e-06 LNL LOS 1 2.93200e-03 2.71700e-06 LNL LP2 1 4.43800e-03 9.46000e-06 LNL LP3 1 5.42500e-03 1.15600e-05 LNL LC3 1 5.60100e-03 1.19400e-05 LNL LC2 1 4.46600e-03 8.41100e-06 LCLC 1 4.88800e-03 1.35900e-05 LC LH1 1 4.43900e-03 1.28400e-05 LC LH2 1 5.85100e-03 1.83700e-05 LCLP 1 6.69100e-03 1.84600e-05 LC LOS 1 3.53900e-03 5.03800e-06 LC LP2 1 5.35900e-03 1.75400e-05 LC LP3 1 6.55000e-03 2.14500e-05 LC LC3 1 6.76300e-03 2.21500e-05 LC LC2 1 5.39100e-03 1.56000e-05 LH1 LH1 1 4.03100e-03 1.21400e-05 LH1 LH2 1 5.31300e-03 1.73600e-05 LH1LP 1 6.07700e-03 1.74400e-05 LH1 LOS 1 3.21400e-03 4.76100e-06 LH1 LP2 1 4.86600e-03 1.65800e-05 LH1 LP3 1 5.94800e-03 2.02700e-05 LH1 LC3 1 6.14200e-03 2.09300e-05 LH1 LC2 1 4.89600e-03 1.47400e-05 LH2 LH2 1 7.00200e-03 2.48300e-05 LH2LP 1 8.00900e-03 2.49500e-05 LH2 LOS 1 4.23600e-03 6.81000e-06 LH2 LP2 1 6.41400e-03 2.37100e-05 LH2 LP3 1 7.83900e-03 2.89900e-05 LH2 LC3 1 8.09500e-03 2.99300e-05 LH2 LC2 1 6.45300e-03 2.10800e-05 LPLP 1 9.16000e-03 2.50700e-05 LP LOS 1 4.84500e-03 6.84200e-06 LP LP2 1 7.33500e-03 2.38300e-05 LP LP3 1 8.96600e-03 2.91300e-05 LP LC3 1 9.25800e-03 3.00800e-05 LP LC2 1 7.38100e-03 2.11900e-05 LOS LOS 1 2.56300e-03 1.86800e-06 LOS LP2 1 3.88000e-03 6.50400e-06 LOS LP3 1 4.74300e-03 7.95100e-06 LOS LC3 1 4.89700e-03 8.21000e-06 LOS LC2 1 3.90400e-03 5.78200e-06 LP2 LP2 1 5.87400e-03 2.26500e-05 LP2 LP3 1 7.18000e-03 2.76900e-05 LP2 LC3 1 7.41400e-03 2.85900e-05 LP2 LC2 1 5.91000e-03 2.01400e-05 LP3 LP3 1 8.77700e-03 3.38500e-05 LP3 LC3 1 9.06200e-03 3.49500e-05 LP3 LC2 1 7.22400e-03 2.46200e-05 LC3 LC3 1 9.35700e-03 3.60900e-05 LC3 LC2 1 7.45900e-03 2.54200e-05 LC2 LC2 1 5.94700e-03 1.79000e-05 ;; lipid-SPC/SPCE interactions LOOW1 2.50200e-03 2.06700e-06 LOMOW1 2.50200e-03 2.06700e-06 LNLOW1 2.98000e-03 3.25900e-06 LCOW1 3.59800e-03 6.04400e-06 LH1OW1 3.26800e-03 5.71200e-06 LH2OW1 4.30700e-03 8.17000e-06 LPOW1 4.92600e-03 8.21000e-06 LOSOW1 2.60500e-03 2.24100e-06 LP2OW1 3.94400e-03 7.80300e-06 LP3OW1 4.82100e-03 9.53900e-06 LC3OW1 4.97800e-03 9.85000e-06 LC2OW1 3.96900e-03 6.93800e-06 [ pairtypes ] ; ijfunc
[gmx-users] "Atomtype OW not found"
I m doning membrane protein simulation , in POPE environment using this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html when I run command: grompp -f minim.mdp -c pope.gro -p topol_pope.top -o em.tpr I always facing this error "Atomtype OW not found" help me ! with regards: shikha agarwal IIIT-A (bioinformatics) -- 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] simulation of membrane protein
Hi, I have a problem with Gromacs. I want to do MD simulations with my membrane proteïn in a POPE-membrane. Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I want to add ions. But when I use grompp to get a .tpr file for genion, Gromacs fives the following error: /Program grompp, VERSION 4.0.7 Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/ /Fatal error: No molecules were defined in the system / help me. shikha agarwal IIIT-A -- 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] simulation of membrane protein
I am trying to simulate a theorical model of a membrane protein in explicit lipid bilayer membrane environment (DMPC or POPC), I have the pdb files of this protein and membrane , I have to topolies files this lipids (dmpc.ip or popc.itp). How we can create merged topology of lipid and protein and do simulation step by step. Anybody could help ? thank you very much ! with regards : shikha agarwal IIIT-A -- 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] simulation of membrane protein
I am beginner in the GROMACS I am trying to simulate a theorical model of a membrane protein in explicit lipid bilayer membrane environment (DMPC or POPC), I have the pdb files of this protein and membrane , I have to topolies files this lipids (dmpc.ip or popc.itp). How we can create merged topology of lipid and protein and do simulation step by step. Anybody could help ? thank you very much ! -- 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
