Dear Gmx Users, I extended a previously ran 10ns simulation by another 15ns by using the following commands :- tpbconv -s mdrun.tpr -extend 15000 -o next.tpr mpirun -np 24 mdrun -s next.tpr -cpi mdrun.cpt -append -v
The number of frames for 10ns simulation were (5001) and when I checked the extended simulation for the number of frames using gmxcheck, I still shows the same number of frames. I want to know does the new frames got appended into old mdrun.trr file as I didn't find any new files, after the simulation got complete...?? Please reply as I am worried whether I made a mistake during the run or I have to repeat everything again ?? The new md.log that was created during extension run says that It has finished the job .... Here's the output of that file :- <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 7500001 steps using 1500001 frames Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 7.43320e+03 4.33773e+02 3.13712e+03 5.20755e+03 2.55855e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 1.37057e+05 -3.56695e+03 -8.60656e+05 -1.20018e+05 -8.05388e+05 Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) 1.29739e+05 -6.75649e+05 3.00003e+02 -2.30179e+02 1.02839e+00 Constr. rmsd 0.00000e+00 Box-X Box-Y Box-Z 8.01379e+00 8.01379e+00 8.01379e+00 Total Virial (kJ/mol) 4.32011e+04 -1.12514e+01 1.49578e+01 -1.14462e+01 4.32407e+04 -1.98925e+01 1.50236e+01 -1.97905e+01 4.32529e+04 Pressure (bar) 7.72036e-01 4.99560e-02 7.81549e-02 6.25159e-02 1.42349e+00 5.98871e-02 7.39076e-02 5.32977e-02 8.89654e-01 Total Dipole (D) -5.60499e+02 -2.55882e+01 2.86784e+02 T-Protein T-non-Protein 2.99927e+02 3.00008e+02 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=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- Coul(T) 2322605.564626 97549433.714 2.2 Coul(T) [W3] 90832.189311 11354023.664 0.3 Coul(T) + LJ 3659809.502236 201289522.623 4.6 Coul(T) + LJ [W3] 619230.648641 85453829.512 2.0 Coul(T) + LJ [W3-W3] 8207387.474804 3135222015.375 71.8 Outer nonbonded loop 1710895.494912 17108954.949 0.4 1,4 nonbonded interactions 71302.509507 6417225.856 0.1 Calc Weights 1170742.656099 42146735.620 1.0 Spread Q Bspline 24975843.330112 49951686.660 1.1 Gather F Bspline 24975843.330112 149855059.981 3.4 3D-FFT 40778435.437124 326227483.497 7.5 Solve PME 612360.081648 39191045.225 0.9 NS-Pairs 5720973.688414 120140447.457 2.7 Reset In Box 26080.500000 78241.500 0.0 CG-CoM 78049.552033 234148.656 0.0 Angles 49455.006594 8308441.108 0.2 Propers 5557.500741 1272667.670 0.0 RB-Dihedrals 55447.507393 13695534.326 0.3 Virial 79264.552843 1426761.951 0.0 Stop-CM 39024.854066 390248.541 0.0 Calc-Ekin 390247.604066 10536685.310 0.2 Lincs 46919.336729 2815160.204 0.1 Lincs-Mat 1003759.241988 4015036.968 0.1 Constraint-V 456988.721878 3655909.775 0.1 Constraint-Vir 82013.920657 1968334.096 0.0 Settle 121050.016140 39099155.213 0.9 ----------------------------------------------------------------------------- Total 4369403789.450 100.0 ----------------------------------------------------------------------------- .... Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 307946.589 307946.589 100.0 3d13h32:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 266.212 14.189 4.209 5.703 Finished mdrun on node 0 Fri Nov 22 23:33:13 2013 Regards ----------- Bharat -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.