Re: [gmx-users] different output generated by continue and discontinue > simulation
Hsin-Lin Chiang wrote: Hi, Mark > > tc-grps = A-chain B-chain drug SOL NA+ > > > > > > > > > > > This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats Thank you for your website. I understand now. > > grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr -o ${n}ps.tpr > > > > > > mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro > > > > You are following neither of the approaches recommended here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > Ya, I'm sorry but my colleborator give me that before. It is similiar to the commends connect position restrained dynamics and MD. You can find grompp read gro and trr of last time frame to make a tpr file of next time frame. I thought this cause the time write on each snapshot is 0, but the dynamics is still processing. Did I miss something? You say the pressure-coupling will be lost in each ps, does it mean that trr file doesn't have this message inside? Pressure coupling information is stored in the .edr file. If you don't pass it to grompp, you lose it. The better method is to use a checkpoint (.cpt) file, which contains everything necessary to accurately continue the simulation. > > Theses two data generated by different ways are totaly different. > > > > Here I mean different is not on the number buy mean the tendency of figure. > > > > > > > > > > > > See http://www.gromacs.org/Documentation/Terminology/Reproducibility Ya, I know this since last time you show me this web in mailing list. Thank you again. But the different between these two outputs is totaly different. I have four systems with different parameter gen_seed. First is always unstable and irregular, but second is stable and regular. It sounds like you have an unstable system, that, under certain favorable conditions, seems to work, but in other cases, doesn't. I'd investigate why the first system is failing, since it probably really is a problem in all of them. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > On the contrary, the second method generate a stable movie and fluctuation of interaction energy. > > > > Theotically these two should be the same, right? > > > > > > > > > > > > The second is probably happier about not losing the pressure-coupling information every 1ns. However only much > much longer trajectories should show mutual convergence, and the movie is not a reasonable way to look for it. > > Mark Sorry I don't understand you here. Do you mean second way seems to more correct? Not correct, but rather not yet suffering from the same problem. And what kind of mutual convergence you mean here? Systems only converge reliably over long time periods, i.e. in theory, independent observations can only be reliably obtained over sufficient time. -Justin Does It mean I can try to find mutual convergence in output of second way? I'm sorry for my stupid and poor English. Sincerely yours, Hsin-Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] different output generated by continue and discontinue > simulation
Hi, Mark > > tc-grps > > = A-chain B-chain drug SOL NA+ > > > > > > > > > > > This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats Thank you for your website. I understand now. > > grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t > > ${n-1}ps.trr -o ${n}ps.tpr > > > > > > mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro > > > > You are following neither of the approaches recommended here > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > Ya, I'm sorry but my colleborator give me that before. It is similiar to the commends connect position restrained dynamics and MD. You can find grompp read gro and trr of last time frame to make a tpr file of next time frame. I thought this cause the time write on each snapshot is 0, but the dynamics is still processing. Did I miss something? You say the pressure-coupling will be lost in each ps, does it mean that trr file doesn't have this message inside? > > Theses two data generated by different ways are totaly different. > > > > Here I mean different is not on the number buy mean the tendency of figure. > > > > > > > > > > > > See http://www.gromacs.org/Documentation/Terminology/Reproducibility Ya, I know this since last time you show me this web in mailing list. Thank you again. But the different between these two outputs is totaly different. I have four systems with different parameter gen_seed. First is always unstable and irregular, but second is stable and regular. > > On the contrary, the second method generate a stable movie and fluctuation > > of interaction energy. > > > > Theotically these two should be the same, right? > > > > > > > > > > > > The second is probably happier about not losing the pressure-coupling > information every 1ns. However only much > much longer trajectories should show mutual convergence, and the movie is not > a reasonable way to look for it. > > Mark Sorry I don't understand you here. Do you mean second way seems to more correct? And what kind of mutual convergence you mean here? Does It mean I can try to find mutual convergence in output of second way? I'm sorry for my stupid and poor English. Sincerely yours, Hsin-Lin -- 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
Re: [gmx-users] different output generated by continue and discontinue simulation
On 12/16/10, Hsin-Lin Chiang wrote: > > > > > > > > > > Hi, > > > > My gromacs version is 4.0.5. > > I used grompp to generate tpr for 1ps simulation in this way > > grompp -f md1.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 1ps.tpr > > mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro > > Here is my md1.mdp file: > > ; > > title = ttt > > cpp = /lib/cpp > > constraints = hbonds > > ;define = -DFLEX_SPC > > integrator = md > > emtol = 100.0 > > emstep = 0.005 > > dt = 0.002 ; ps ! > > nsteps = 500 ; total 1 ps > > nstcomm = 500 > > nstxout = 500 > > nstvout = 500 > > nstfout = 500 > > nstlog = 500 > > nstenergy = 500 > > nstlist = 5 > > ns_type = grid > > rlist = 1. > > rcoulomb = 1. > > rvdw = 1. > > coulombtype = PME > > fourierspacing = 0.12 > > pme_order = 4 > > optimize_fft = yes > > > > > > > > > > > Tcoupl = v-rescale > > tc-grps = A-chain B-chain drug SOL NA+ > > > > > This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats > > > > > > ;tau_t = 0.1 0.1 > > tau_t = 0.2 0.2 0.2 0.2 0.2 > > ref_t = 300.00 300.00 300.00 300.00 300.00 > > energygrps = A-chain B-chain drug SOL NA+ > > Pcoupl = berendsen > > Pcoupltype = isotropic > > ;tau_p = 0.1 > > tau_p = 0.25 > > compressibility = 5.4e-5 > > ref_p = 1.0 > > gen_vel = yes > > gen_temp = 300.00 > > gen_seed = 173531 > > > > -- > > Then I execute below loop in other 5 times for the totaly 60ns > trajectories. > > grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr > -o ${n}ps.tpr > > > mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro > > > > > You are following neither of the approaches recommended here http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > > > > > The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no. > > Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to > continue.(I didn't really use this commend $(n-1) in bash script, it won't > work.) > > > > I change the other way to run parallel simulation on the same system for > double check since above script is difficult to parallelize in public > computer. > > The new method is: > > grompp -f md60ns.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o > 60ns.tpr > > mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c > 60ns.gro > > The only different between md1.mdp and md60ns.mdp is nstep=3000 in > md60ns.mdp. > > > > Theses two data generated by different ways are totaly different. > > Here I mean different is not on the number buy mean the tendency of figure. > > > > > See http://www.gromacs.org/Documentation/Terminology/Reproducibility > > > > > > In the movie of first method, protein runs violently and go outside the > periodic boundary and then split by cubic edge. > > The interaction energy within protein also fluctuate in an unstable way. > > > > On the contrary, the second method generate a stable movie and fluctuation of > interaction energy. > > Theotically these two should be the same, right? > > > > > The second is probably happier about not losing the pressure-coupling information every 1ns. However only much much longer trajectories should show mutual convergence, and the movie is not a reasonable way to look for it. Mark > > > > > > Is anything wrong in my work? > > > > Sincerely yours, > > Hsin-Lin > > > > > > > > > > > > -- 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] different output generated by continue and discontinue simulation
Sorry for the abnormal code. I have fixed that. --- Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here is my md1.mdp file: ; title = ttt cpp = /lib/cpp constraints = hbons ;define = -DFLEX_SPC integrator = md emtol = 100.0 emstep = 0.005 dt = 0.002 ; ps! nsteps = 500 ; total 1ps nstcomm = 500 ntsxout = 500 ntsvout = 500 ntsfout = 500 ntslog = 500 nstenergy = 500 nstlist = 5 ns_type = grid rlist = 1. rcoulomb = 1. rvdw = 1. coulombtype = PME fourierspacing = 0.12 pme_order = 4 optimize_fft = yes Tcoupl = v-rescale rc-grps = A-chain B-chain drug SOL NA+ ;tau_t = 0.1 0.1 tau_t =0.2 0.2 0.2 0.2 ref_t = 300.00 300.00 300.00 300.0 300.00 energygrps = A-chain B-chain druhg SOL NA+ Pcoupl = berendsen Pcoupltype = isotropic ;tau_p = 0.1 tau_p = 0.25 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.00 gen_seed = 173531 gen_seed = 173531 -- Then I execute below loop in other 5 times for the totaly 60ns trajectories. grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr -o ${n}ps.tpr mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no. Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to continue.(I didn't really use this commend $(n-1) in bash script, it won't work.) I change the other way to run parallel simulation on the same system fordouble check since above script is difficult to parallelize in public computer. The new method is: grompp -f md60ns.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 60ns.tpr mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c 60ns.gro The only different between md1.mdp and md60ns.mdp is nstep=3000 in md60ns.mdp. Theses two data generated by different ways are totaly different. Here I mean different is not on the number buy mean the tendency of figure. In the movie of first method, protein runs violently and go outside the periodic boundary and then split by cubic edge. The interaction energy within protein also fluctuate in an unstable way. On the contrary, the second method generate a stable movie and fluctuation of interaction energy. Theotically these two should be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin --- End of Forwarded Message --- -- 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] different output generated by continue and discontinue simulation
Sorry for the abnormal code. I have fixed that. --- Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here is my md1.mdp file: ; title = ttt cpp = /lib/cpp constraints = hbonds ;define = -DFLEX_SPC integrator = md emtol = 100.0 emstep = 0.005 dt = 0.002 ; ps ! nsteps = 500 ; total 1 ps nstcomm = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid rlist = 1. rcoulomb = 1. rvdw = 1. coulombtype = PME fourierspacing = 0.12 pme_order = 4 optimize_fft = yes Tcoupl = v-rescale tc-grps = A-chain B-chain drug SOL NA+ ;tau_t = 0.1 0.1 tau_t = 0.2 0.2 0.2 0.2 0.2 ref_t = 300.00 300.00 300.00 300.00 300.00 energygrps = A-chain B-chain drug SOL NA+ Pcoupl = berendsen Pcoupltype = isotropic ;tau_p = 0.1 tau_p = 0.25 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.00 gen_seed = 173531 -- Then I execute below loop in other 5 times for the totaly 60ns trajectories. grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr -o ${n}ps.tpr mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no. Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to continue.(I didn't really use this commend $(n-1) in bash script, it won't work.) I change the other way to run parallel simulation on the same system fordouble check since above script is difficult to parallelize in public computer. The new method is: grompp -f md60ns.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 60ns.tpr mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c 60ns.gro The only different between md1.mdp and md60ns.mdp is nstep=3000 in md60ns.mdp. Theses two data generated by different ways are totaly different. Here I mean different is not on the number buy mean the tendency of figure. In the movie of first method, protein runs violently and go outside the periodic boundary and then split by cubic edge. The interaction energy within protein also fluctuate in an unstable way. On the contrary, the second method generate a stable movie and fluctuation of interaction energy. Theotically these two should be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- 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] different output generated by continue and discontinue simulation
Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here is my md1.mdp file: ; title = ttt cpp = /lib/cpp constraints = hbonds ;define = -DFLEX_SPC integrator = md emtol = 100.0 emstep = 0.005 dt = 0.002 ; ps ! nsteps = 500 ; total 1 ps nstcomm = 500 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid rlist = 1. rcoulomb = 1. rvdw = 1. coulombtype = PME fourierspacing = 0.12 pme_order = 4 optimize_fft = yes Tcoupl = v-rescale tc-grps = A-chain B-chain drug SOL NA+ ;tau_t = 0.1 0.1 tau_t = 0.2 0.2 0.2 0.2 0.2 ref_t = 300.00 300.00 300.00 300.00 300.00 energygrps = A-chain B-chain drug SOL NA+ Pcoupl = berendsen Pcoupltype = isotropic ;tau_p = 0.1 tau_p = 0.25 compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.00 gen_seed = 173531 -- Then I execute below loop in other 5 times for the totaly 60ns trajectories. grompp -f md2.mdp -n index.ndx -p topol.top -c ${n-1}ps.gro -t ${n-1}ps.trr -o ${n}ps.tpr mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no. Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory to continue.(I didn't really use this commend $(n-1) in bash script, it won't work.) I change the other way to run parallel simulation on the same system for double check since above script is difficult to parallelize in public computer. The new method is: grompp -f md60ns.mdp -n index.ndx -p topol.top -c 0ps.gro -t 0ps.trr -o 60ns.tpr mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c 60ns.gro The only different between md1.mdp and md60ns.mdp is nstep=3000 in md60ns.mdp. Theses two data generated by different ways are totaly different. Here I mean different is not on the number buy mean the tendency of figure. In the movie of first method, protein runs violently and go outside the periodic boundary and then split by cubic edge. The interaction energy within protein also fluctuate in an unstable way. On the contrary, the second method generate a stable movie and fluctuation of interaction energy. Theotically these two should be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- 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