[gmx-users] Simulation Box type
Dear All, I want to opt for the rhombic dodecahedron box in my simulation of a protein. I am using the following command to select the type of the box editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron but after this if I'm seeing this protein system within the box in VMD but its not showing that dodecahedron box, instead showing rectangular one. I don't know whether I am giving the wrong command or it's coming out from VMD software. So can anyone give suggestion regarding this problem so that I can make myself confirmed by seeing the exact box, I need to have, prior to the simulation. Thanks in advance, Tarak -- Tarak Karmakar Molecular Simulation Lab. C.P.M.U JNCASR -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation Box type
On 17/07/2012 4:16 PM, tarak karmakar wrote: Dear All, I want to opt for the rhombic dodecahedron box in my simulation of a protein. I am using the following command to select the type of the box editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron but after this if I'm seeing this protein system within the box in VMD but its not showing that dodecahedron box, instead showing rectangular one. I don't know whether I am giving the wrong command or it's coming out from VMD software. So can anyone give suggestion regarding this problem so that I can make myself confirmed by seeing the exact box, I need to have, prior to the simulation. This is normal (discussed often in the archives). The box is specified by its vectors, not by the atomic coordinates, and the triclinic box you can see with VMD is equivalent to what you chose (e.g. a 2D tiling with hexagons can be represented as a 2D tiling of rhombuses). You can see trjconv -h about -ur to change the coordinates for visualization purposes. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] genconf command
Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then genconf was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one? Thank you very much. Best regards, Cuong -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] DANGLING BOND IN GOLD-PROTEIN SIMULATION
HELLO I want simulate gold-protein complex by Golp forcefield. but when I use pdb_gmx I came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. PLEASE HELP ME regards, Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] why Blue Gene/Q is so slow?
Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: 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 - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6 Virial 4.636254 83.453 0.0 Update 44.4788941378.846 0.2 Stop-CM 4.455894 44.559 0.0 Calc-Ekin 44.4877881201.170 0.1 Lincs 44.9516302697.098 0.3 Lincs-Mat 261.8225521047.290 0.1 Constraint-V44.951630 359.613 0.0 Constraint-Vir 2.251163 54.028 0.0 - Total 808731.820 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 660.5 av. #atoms communicated per step for LINCS: 2 x 34.3 Average load imbalance: 1.7 % Part of the total run time spent waiting due to load imbalance: 1.4 % 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 % --- Domain decomp. 8502 59.421 37.1 0.5 DD comm. load 8 80.0040.0 0.0 Comm. coord. 8 5001 16.575 10.4 0.2 Neighbor
[gmx-users] Re: Error in Membrane simulations with POPC bilayer
Hi Justin, I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 What do they really mean? Is the system safe with these notes? Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-Membrane-simulations-with-POPC-bilayer-tp4999161p4999483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genconf command
On 17/07/2012 4:32 PM, cuong nguyen wrote: Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then genconf was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one? Start with genconf -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why Blue Gene/Q is so slow?
On 17/07/2012 5:00 PM, DeChang Li wrote: Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Your workstation is running highly effective optimized SSE loops. BlueGene/Q is not using its multiple FPU because that code hasn't been written (for explicit or implicit solvation), and BlueGene's processors are probably slower too. Mark Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: 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 - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6 Virial 4.636254 83.453 0.0 Update 44.4788941378.846 0.2 Stop-CM 4.455894 44.559 0.0 Calc-Ekin 44.4877881201.170 0.1 Lincs 44.9516302697.098 0.3 Lincs-Mat 261.8225521047.290 0.1 Constraint-V44.951630 359.613 0.0 Constraint-Vir 2.251163 54.028 0.0 - Total 808731.820 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 660.5 av. #atoms communicated per step for LINCS: 2 x 34.3 Average load imbalance: 1.7 % Part of the total run time spent waiting due to load imbalance: 1.4 % 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
Re: [gmx-users] genconf command
Dear cuong nguyen.. I think use following commands. Try editconf -rotate for rotaion angle along axis along these use -center co-ordinate if you want to place canter of box at particular position Try editconf -translate For translation along axis On Tue, Jul 17, 2012 at 2:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/07/2012 4:32 PM, cuong nguyen wrote: Dear Gmx-users, I created a box size 4 4 2 and named layer.gro. Then genconf was used to doulble this box: genconf -f layer.gro -o 2layers.gro -nbox 1 1 2 -dist 0 0 8 However, the copied box has the same direction as the original box. Could you please help me to rotate 180 degrees the copied one? Start with genconf -h. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Re: why Blue Gene/Q is so slow? (Mark Abraham)
-- Message: 8 Date: Tue, 17 Jul 2012 18:40:05 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] why Blue Gene/Q is so slow? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 500524e5.9050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 17/07/2012 5:00 PM, DeChang Li wrote: Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Your workstation is running highly effective optimized SSE loops. BlueGene/Q is not using its multiple FPU because that code hasn't been written (for explicit or implicit solvation), and BlueGene's processors are probably slower too. Mark That means the code itself causes only 10% speed in BlueGene/Q compared with intel CPUs workstation? Is there any method to improve the speed in BG/Q? Dechang Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: 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 - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6 Virial 4.636254 83.453 0.0 Update 44.4788941378.846 0.2 Stop-CM 4.455894 44.559 0.0 Calc-Ekin 44.4877881201.170 0.1 Lincs 44.9516302697.098 0.3 Lincs-Mat 261.8225521047.290 0.1 Constraint-V44.951630 359.613 0.0 Constraint-Vir 2.251163 54.028 0.0
Re: [gmx-users] Re: Error in Membrane simulations with POPC bilayer
On 7/17/12 4:05 AM, J Peterson wrote: Hi Justin, I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy http://manual.gromacs.org/online/mdp_opt.html#out nstcalcenergy tries to improve performance by reducing global communication. If you set nstcomm to a more frequent interval of steps, you're doing global communication more frequently, hence making nstcalcenergy relatively pointless, so grompp sets them both to nstcalcenergy for efficiency. NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 As stated in the manual, NH chains 1 can only be used with a velocity verlet integrator. What do they really mean? Is the system safe with these notes? Yes. These are normal messages. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Any ways to read/convert .g96 file format and keep the precision?
Dear All, I rephrase my question (for the original see below). Is there any (easy) way to give gromacs (mdrun -rerun) accurate coordinates for a single point calculation (to get accurate energy and forces)? The accuracy of .pdb and .gro formats is not sufficient and .g96 format reading seems to be broken. Terveisin, Markus Are there any ways to read/convert positions in .g96 file format and keep the precision (%15.9f) for a structure to be read by mdrun -rerun myfile.g96 ? I get an annoying error message: Reading trajectories in .g96 format is broken. Please use a different file format. with mdrun and trjconv -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: Karjaan lukio --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Gromacs-Orca QMMM LJ coefficients problem
Hello, I've been trying some time now to run a QMMM calculation with gromacs and orca on a system of 5000 atoms with the QM system being ~300 atoms. Setting up the calculation with bOpt = yes and 1 minim step in the .mdp file produces some problems. Orca does the calculation without taking into account the LJ coefficients. The .LJ file should be generated by gromacs prior to the calculation so Orca uses it for the QM atoms optimization right? ( I have seen that there should be LJ and LJ.Excl files) However these files are not generated and Orca does a perfect optimization of 300 cycles but without taking into account any Lennard Jones input. So in every optimization step Orca skips VdW correction (No LJ-filename given... skipping VDW correction) because it doesn't find the LJ file and continues the QM optimization in the absence of the MM system. I am running gromacs 4.5.5 and after many many tries, I cannot see the .LJ file. Not in the beginning, nor during the calculation in the woking directory. Could there be an explanation why gromacs does not generate this file? Best Minos I attach my mdp file: - title = Yo ; a string cpp = /lib/cpp ; c-preprocessor integrator = cg ; ;integrator = l-bfgs rlist = 1.0 ; cut-off for ns rvdw= 1.4 ; cut-off for vdw rcoulomb= 1.5 ; cut-off for coulomb ; Energy minimizing stuff ; nsteps = 1 emtol = 100 emstep = 0.1 nstxout = 1 nstfout = 1 nstlog - 1 nstvout = 1 nstxtcout= 1 nstenergy= 1 QMMM = yes QMMM-grps= QMatoms QMMMscheme = ONIOM QMbasis = 6-31g* QMmethod = RHF QMcharge = 1 QMmult = 1 bOpt = yes and ORCAINFO file: ! RHF 6-31g* SV(P) moread %moinp orbitals.gbw %pointcharges charges.pc %pal nprocs 24 end and the .inp file Orca needs that is generated by gromacs: #input-file generated by gromacs !QMMMOpt TightSCF ! RHF 6-31g* SV(P) moread %moinp orbitals.gbw %pointcharges charges.pc %pal nprocs 24 end %geom . . . . . -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-Orca-QMMM-LJ-coefficients-problem-tp4999490.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Any ways to read/convert .g96 file format and keep the precision?
On 7/17/12 7:16 AM, Markus Kaukonen wrote: Dear All, I rephrase my question (for the original see below). Is there any (easy) way to give gromacs (mdrun -rerun) accurate coordinates for a single point calculation (to get accurate energy and forces)? The accuracy of .pdb and .gro formats is not sufficient and .g96 format reading seems to be broken. Convert the .g96 file to .trr format. Double precision may be necessary and will certainly give the greatest possible accuracy. -Justin Terveisin, Markus Are there any ways to read/convert positions in .g96 file format and keep the precision (%15.9f) for a structure to be read by mdrun -rerun myfile.g96 ? I get an annoying error message: Reading trajectories in .g96 format is broken. Please use a different file format. with mdrun and trjconv -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Error in Membrane simulations with POPC bilayer (
I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 What do they really mean? Is the system safe with these notes? Peterson J Peterson J -- These are not errors, as you say in the title, but just notes, and I think they mean exactly what is written. What force field are you using for a POPC bilayer? Just curious... Cordially, Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 speed up equilibrating the density of bulk system?
Dear gmxers, I am trying to generate one polymer melt from one big enough box using NPT MD in gmx. I find that the density of system varies very slow. Could you please give me some hints about how to speed up this process? Thanks a lot for any reply. Yours sincerely, Chaofu Wu. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Gromacs-Orca QMMM LJ coefficients problem
Well, the problem was solved at the end, please don't bother answering. Following the advise of one of the Orca developers, Christoph, I changed QMMMscheme to normal instead of ONIOM and disabled periodic boundary conditions. Now the files are extracted normally. for further reference, one should get in the working directory these files, important for the calculation: basename.LJ basename.LJ.excl basename.pc basename.pcgrad M. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-Orca-QMMM-LJ-coefficients-problem-tp4999490p4999494.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Short question about 1-4, 1-5+ interactions
Dear all, I have a question about internal bond interactions within a molecule. I understand that 1-4 interactions can be scaled with nbfunc. But I wonder: 1. What is the default for 1-5 and larger interactions in Gromacs? Are the LJ and charge interactions included (i.e., not scaled)? I'm specifically interested in reproducing OPLS United-Atom molecules from Jorgensen's 1986 OPLS paper. He doesn't mention anything about scaling in that paper though so I guess he's not doing any scaling of any inner-molecule interactions at all (please someone correct me if this is obviously wrong). 2. Is there any way to scale the 1-5+ interactions in Gromacs? Thanks in advance! I appreciate any help. Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to speed up equilibrating the density of bulk system?
A variabvle thermostat that increases from 180 K to 300 K over cycles of 100-1 Original-Nachricht Datum: Tue, 17 Jul 2012 20:40:12 +0800 Von: Wu Chaofu xiaowu...@gmail.com An: gmx-users@gromacs.org Betreff: [gmx-users] How to speed up equilibrating the density of bulk system? Dear gmxers, I am trying to generate one polymer melt from one big enough box using NPT MD in gmx. I find that the density of system varies very slow. Could you please give me some hints about how to speed up this process? Thanks a lot for any reply. Yours sincerely, Chaofu Wu. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Re: why Blue Gene/Q is so slow? (Mark Abraham)
On 17/07/2012 7:06 PM, DeChang Li wrote: -- Message: 8 Date: Tue, 17 Jul 2012 18:40:05 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] why Blue Gene/Q is so slow? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 500524e5.9050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 17/07/2012 5:00 PM, DeChang Li wrote: Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's wrong in my simulation? Any suggestion will be appreciated. Your workstation is running highly effective optimized SSE loops. BlueGene/Q is not using its multiple FPU because that code hasn't been written (for explicit or implicit solvation), and BlueGene's processors are probably slower too. Mark That means the code itself causes only 10% speed in BlueGene/Q compared with intel CPUs workstation? You'd see a comparable decrease if you would turn off the SSE optimization on your workstation, but perhaps not as severe. There's art and skill in making code run fast, and it's very rare that you don't need to target a specific architecture to achieve it. Is there any method to improve the speed in BG/Q? Write the optimized code ;-) Also, use more of the machine - you can probably get down to 500 atoms/core or below. There will be a limit beyond which it's impossible to go (or be effective). You can try simulating without cut-offs (see parts of manual 7.3 and mailing list discussions) which uses different all-vs-all inner loops, but your system might be too large for that to be useful. Mark Dechang Following is my md.mdp file: constraints= hbonds constraint_algorithm = LINCS lincs_order= 4 comm_mode = Angular comm_grps = system integrator = sd ;annealing = single single ;annealing_npoints = 2 2 ;annealing_time = 0 500 0 500 ;annealing_temp = 200 300 200 300 dt = 0.002 ; ps ! nsteps = 500 ; total 5000 ps. nstcomm= 10 nstcalcenergy = 10 nstxout= 1 ; collect data every 1 ps nstenergy = 1 nstvout= 1 nstlog = 1000 ;nstxtcout = 5 ;xtc_grps = system nstfout= 0 nstlist= 10 ns_type= grid pbc= no rlist = 1.2 coulombtype= cut-off rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma ;DispCorr = EnerPres ; Berendsen temperature coupling is on in two groups Tcoupl = tau_t = 0.5 tc-grps= system ref_t = 300 ; Pressure coupling is on Pcoupl = no ;berendsen tau_p = 1.0 compressibility= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel= yes gen_temp = 300 gen_seed = -1 implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 1.2 sa_surface_tension = 2.25936 Here is the preformace info: 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 - Generalized Born Coulomb61.4828922951.179 0.4 GB Coulomb + LJ 2565.481100 156494.34719.4 Outer nonbonded loop 152.2685461522.685 0.2 1,4 nonbonded interactions 116.143224 10452.890 1.3 Born radii (HCT/OBC) 2868.34 524884.66964.9 Born force chain rule 2868.34 43023.334 5.3 NS-Pairs 516.814696 10853.109 1.3 Reset In Box 4.464788 13.394 0.0 CG-CoM 4.482576 13.448 0.0 Bonds 22.1744341308.292 0.2 Angles 80.586114 13538.467 1.7 Propers160.742142 36809.951 4.6
[gmx-users] Re: Any ways to read/convert .g96 file format and keep the precision? Or any way to give accurate coordinates?
Convert the .g96 file to .trr format. Double precision may be necessary and will certainly give the greatest possible accuracy. -Justin I try trjconv -f gromacs.g96 -o test.trr and get Program trjconv, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is there some other way to convert format (g96 - trr)? Or any other easy way to give accurate coordinates? Or do I have a too old version of gromacs (4.5.5) ? Terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: Karjaan lukio --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Any ways to read/convert .g96 file format and keep the precision? Or any way to give accurate coordinates?
On 7/17/12 12:51 PM, Markus Kaukonen wrote: Convert the .g96 file to .trr format. Double precision may be necessary and will certainly give the greatest possible accuracy. -Justin I try trjconv -f gromacs.g96 -o test.trr and get Program trjconv, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Is there some other way to convert format (g96 - trr)? Not to my knowledge. Among other things, that's what trjconv is designed for. Or any other easy way to give accurate coordinates? Not to my knowledge. Or do I have a too old version of gromacs (4.5.5) ? 4.5.5 is the newest version, and the inability to read .g96 is still present in the latest development code. I suspect no one has had a need for .g96 format in quite some time, so it has been ignored. The issue will certainly remain unaddressed until you or someone else posts a feature request on redmine.gromacs.org. I don't know if it will be fixed before the 4.6 release (whenever that is) due to a feature freeze that has been in place for quite some time. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to speed up equilibrating the density of bulk system?
Hi, You can scale the system with editconf to some density and energy minimize, and equilibrate 1000 steps or so in NVT. Do this with small scaling factors, repeating until tje density is correct. You might want to run at a relatively high temperature. Cheers, Tsjerk On Tue, Jul 17, 2012 at 2:40 PM, Wu Chaofu xiaowu...@gmail.com wrote: Dear gmxers, I am trying to generate one polymer melt from one big enough box using NPT MD in gmx. I find that the density of system varies very slow. Could you please give me some hints about how to speed up this process? Thanks a lot for any reply. Yours sincerely, Chaofu Wu. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Measuring hydrogen bonding in a specific region
Hi all, I have a system that consists of two distinct reservoirs filled with water+NaCl connected by a CNT. I want to measure the average number of hydrogen bonds per water in each reservoir as a function of time, but my current workflow for this is far too time-consuming to get any significant resolution: -Have trjconv dump frames to separate .gro files (for example, in 10ns increments) -use g_select to create a .ndx file with groups for the waters in either reservoir -run g_hbond on the .gro file with the appropriate .ndx file, record the number of hbonds and the number of donors for each reservoir Is there any way I could automate/improve this process? I have ten of these simulations longer than 100 ns to analyze, and I just need more data points than I can crank out manually. Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Measuring hydrogen bonding in a specific region
On 7/17/12 4:37 PM, Alex Marshall wrote: Hi all, I have a system that consists of two distinct reservoirs filled with water+NaCl connected by a CNT. I want to measure the average number of hydrogen bonds per water in each reservoir as a function of time, but my current workflow for this is far too time-consuming to get any significant resolution: -Have trjconv dump frames to separate .gro files (for example, in 10ns increments) -use g_select to create a .ndx file with groups for the waters in either reservoir -run g_hbond on the .gro file with the appropriate .ndx file, record the number of hbonds and the number of donors for each reservoir Is there any way I could automate/improve this process? I have ten of these simulations longer than 100 ns to analyze, and I just need more data points than I can crank out manually. g_select allows you to create dynamic indices. The resulting index file cannot be used automatically by any tool, but it will give you a list of all atoms that satisfy whatever criteria you specify (e.g. within certain coordinate ranges that indicate the reservoirs). One run through the trajectory will generate all the index groups, then a shell script can be used to loop through all of the index groups (one per frame) with tools like g_hbond. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Measuring hydrogen bonding in a specific region
Hi Justin, I am just curious, do you have experience writing such a shell script to iterate over the index files (one per frame)? I am just curious, because I have been trying this, and I have found it very difficult to do using bash. Do you use a different shell language? Also, I wonder if anyone has ever posted such a shell script on this list. When I look through the archives, I don't see one, but I could be wrong. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Measuring hydrogen bonding in a specific region
On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because I
have been trying this, and I have found it very difficult to do using bash.
Do you use a different shell language?
Also, I wonder if anyone has ever posted such a shell script on this list.
When I look through the archives, I don't see one, but I could be wrong.
Assume we have 100 groups of arbitrary size and a fixed group (index group 0) in
the index file to which we wish to calculate hydrogen bonds. Then assume we
have 100 separate files (from trjconv -sep or whatever else) numbered
sequentially, i.e. conf1.gro, conf2.gro...conf100.gro. A simple bash script
that runs through the index groups corresponding to each of these coordinate
files would be something like:
#!/bin/bash
for i in {1..100}
do
echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx
done
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Measuring hydrogen bonding in a specific region
Thanks Justin, this is great.
On Tue, Jul 17, 2012 at 5:07 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because
I
have been trying this, and I have found it very difficult to do using
bash.
Do you use a different shell language?
Also, I wonder if anyone has ever posted such a shell script on this list.
When I look through the archives, I don't see one, but I could be wrong.
Assume we have 100 groups of arbitrary size and a fixed group (index group
0) in the index file to which we wish to calculate hydrogen bonds. Then
assume we have 100 separate files (from trjconv -sep or whatever else)
numbered sequentially, i.e. conf1.gro, conf2.gro...conf100.gro. A simple
bash script that runs through the index groups corresponding to each of
these coordinate files would be something like:
#!/bin/bash
for i in {1..100}
do
echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx
done
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
--
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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: Peptide folding simulation
Hi, I tried again simulating the same peptide with OPLS FF for 2000 ns time duration. I used VMD for the secondary structure analysis and trajectory visualization. This time I was able to get folding events but the residues that are should be beta strands were helical for most of the time during simulation. Is it because of the parameters or what else could have gone wrong ?? BHARAT -- View this message in context: http://gromacs.5086.n6.nabble.com/Peptide-folding-simulation-tp4999215p4999506.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Some interactions seem to be assigned multiple times
and this did not happen with EM? Did you add new atoms/FF parameters to the existing C36 set? On 2012-07-13 02:05:47AM -0700, Shima Arasteh wrote: Dear gmx users, My system is composed of a protein and water. I am working with CHARMM36 and the current version of Gromacs, 4.5.5. For NVT equilibration , I get this error: Software inconsistency error: Some interactions seem to be assigned multiple times Through the mailing list, I just found that some bugs might be the reason of the error, and the Gromacs version should be current. But as I said I use the current version of Gromacs. I really don't have any idea for solving this problem. Any suggestions would be appreciated. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Some interactions seem to be assigned multiple times
I added a new residue by using defined atom types. I did not get this error with EM. This error happened when I just entered the command of #deffnm NVT. Thanks in advance. Sincerely, Shima From: Peter C. Lai p...@uab.edu To: gmx-users@gromacs.org Sent: Wednesday, July 18, 2012 9:00 AM Subject: Re: [gmx-users] Some interactions seem to be assigned multiple times and this did not happen with EM? Did you add new atoms/FF parameters to the existing C36 set? On 2012-07-13 02:05:47AM -0700, Shima Arasteh wrote: Dear gmx users, My system is composed of a protein and water. I am working with CHARMM36 and the current version of Gromacs, 4.5.5. For NVT equilibration , I get this error: Software inconsistency error: Some interactions seem to be assigned multiple times Through the mailing list, I just found that some bugs might be the reason of the error, and the Gromacs version should be current. But as I said I use the current version of Gromacs. I really don't have any idea for solving this problem. Any suggestions would be appreciated. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] mdrun -j still functional?
Has anyone been recently using the coupling feature of mdrun for parameterising? I used it many versions ago and have just been trying to use it today with 4.5.5, however I can't get it to work as it did previously. Currently you can't couple more than one set of charges (seems a bit weird that one since you can't now keep the total charge constant / neutral) or LJ parameters. With single charge it runs and seems to work, however with single LJ I get a segmentation fault. Just wondering if this part of the code is still functional or not? May be it hasn't been updated for a number of versions, developers aren't working on it, so now it is broken? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
