Re: [gmx-users] MD continuation runs in serial but not in parallel
I did not use -shuffle -t to run this. However even when I use -shuffle option the same error occurs. From: Sridhar Acharya <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] MD continuation runs in serial but not in parallel Date: Mon, 03 Jul 2006 17:56:27 +0530 Dear GMX users, I used grompp with -t option to continue a serially run simulation to run in parallel. I have given gen_vel = no in the .mdp file. But mdrun "with -np 2" stops and reports the following error. (md.log file is given below) The same simulation could be continued in serial without any error. What is the cause for this descrepancy? Any parameters to be set? # Going to use C-settle (5335 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.42 4862 4887 0.07 After LINCS 0.49 4880 4881 0.10 Started mdrun on node 0 Mon Jul 3 18:48:47 2006 Initial temperature: 301.39 K Grid: 17 x 14 x 19 cells Step Time Lambda Annealing 00.00.01.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.058480 3573 3574 0.005918 After LINCS 0.000140 3842 3844 0.20 t = 0.000 ps: Water molecule starting at atom 17176 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.10484e+033.58568e+032.61866e+031.41412e+034.86285e+04 LJ (SR) Coulomb (SR) Coulomb (LR) PotentialKinetic En. 2.14166e+08 -5.54411e+05 -1.31762e+052.13544e+08nan Total EnergyTemperature Pressure (bar) nannannan ## -- Did you use the -shuffle option of grompp? With grompp -shuffle -t grompp expectes a shuffled trajectory. Berk. -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] MD continuation runs in serial but not in parallel
From: Sridhar Acharya <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] MD continuation runs in serial but not in parallel Date: Mon, 03 Jul 2006 17:56:27 +0530 Dear GMX users, I used grompp with -t option to continue a serially run simulation to run in parallel. I have given gen_vel = no in the .mdp file. But mdrun "with -np 2" stops and reports the following error. (md.log file is given below) The same simulation could be continued in serial without any error. What is the cause for this descrepancy? Any parameters to be set? # Going to use C-settle (5335 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.42 4862 4887 0.07 After LINCS 0.49 4880 4881 0.10 Started mdrun on node 0 Mon Jul 3 18:48:47 2006 Initial temperature: 301.39 K Grid: 17 x 14 x 19 cells Step Time Lambda Annealing 00.00.01.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.058480 3573 3574 0.005918 After LINCS 0.000140 3842 3844 0.20 t = 0.000 ps: Water molecule starting at atom 17176 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.10484e+033.58568e+032.61866e+031.41412e+034.86285e+04 LJ (SR) Coulomb (SR) Coulomb (LR) PotentialKinetic En. 2.14166e+08 -5.54411e+05 -1.31762e+052.13544e+08nan Total EnergyTemperature Pressure (bar) nannannan ## -- Did you use the -shuffle option of grompp? With grompp -shuffle -t grompp expectes a shuffled trajectory. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD continuation runs in serial but not in parallel
Dear GMX users, I used grompp with -t option to continue a serially run simulation to run in parallel. I have given gen_vel = no in the .mdp file. But mdrun "with -np 2" stops and reports the following error. (md.log file is given below) The same simulation could be continued in serial without any error. What is the cause for this descrepancy? Any parameters to be set? # Going to use C-settle (5335 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.42 4862 4887 0.07 After LINCS 0.49 4880 4881 0.10 Started mdrun on node 0 Mon Jul 3 18:48:47 2006 Initial temperature: 301.39 K Grid: 17 x 14 x 19 cells Step Time Lambda Annealing 00.00.01.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.058480 3573 3574 0.005918 After LINCS 0.000140 3842 3844 0.20 t = 0.000 ps: Water molecule starting at atom 17176 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.10484e+033.58568e+032.61866e+031.41412e+034.86285e+04 LJ (SR) Coulomb (SR) Coulomb (LR) PotentialKinetic En. 2.14166e+08 -5.54411e+05 -1.31762e+052.13544e+08nan Total EnergyTemperature Pressure (bar) nannannan ## -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
