Re: [gmx-users] Results of villin headpiece with AMD 8 core
Mirco,on the modification - nicely done.On the system speed, running Maestro-Desmond one core ) the 1080ti is pegged and at usually 90% power. them folks at Schrodinger know what they are doing. So the base speed is apparently sufficient, its some other factor e.g. the work load distribution that is not optimized.I’ll work with your files tomorrow and let you know how it turns out— thanks Have a a great weekendPaulOn Jan 12, 2019, at 3:11 PM, Wahab Mirco wrote:Hi Paul,thanks for your reply.On 11.01.2019 23:20, paul buscemi wrote:Getting the ion and SOL concentration correct in the top is trickier ( for me ) than it should have been, If you happen to reuse both solvate and genion during the build keeping track of the top is like using a digital rubics cube..! The charge the villin was +1 because after I downloaded it from the pdb I removed all other water and ions - it just made pdb2gmx easier to work with.I simply hand-edited the .gro by making up two ions and put themsomewhere near the corners and added a short energy minimization.Then, I added one line in the .top for the ions.The 1080 scaled nicely with the 1080 ti, these are really nice pieces of hardware. and you are correct, given the choice of increased processors vs faster processors - choose the latter. I have the AMD OC to 4.0 GH and it runs the same model almost as fast as as 32 core AMD at 3.7 GHz.Your system is possibly too slow to saturate the 1080Ti at this smallsystem size. In a much larger system, the lead of the 1080 Ti over the1080 may possibly reach the theoretical expectation.I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day in NPT. And yes, if you can send the pdb, top, and itps I’t would be interesting to compare the two AMDs.I did upload the stuff here + a readme-file. This system is much toolarge for a single box + GPU (for productive runs), but maybe in 5 yearsor so we can watch capillary waves through connected IMD/VMD in real-time ;)=> http://suwos.gibtsfei.net/d.dppc.4096.zipRegardsMirco-- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.-- 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.
Re: [gmx-users] Results of villin headpiece with AMD 8 core
Mirco, on the modification - nicely done. On the system speed, running Maestro-Desmond one core ) the 1080ti is pegged and at usually 90% power. them folks at Schrodinger know what they are doing. So the base speed is apparently sufficient, its some other factor e.g. the work load distribution that is not optimized. I’ll work with your files tomorrow and let you know how it turns out— thanks Have a a great weekend Paul > On Jan 12, 2019, at 3:11 PM, Wahab Mirco > wrote: > > Hi Paul, > > thanks for your reply. > > On 11.01.2019 23:20, paul buscemi wrote: >> Getting the ion and SOL concentration correct in the top is trickier ( for >> me ) than it should have been, If you happen to reuse both solvate and >> genion during the build keeping track of the top is like using a digital >> rubics cube..! The charge the villin was +1 because after I downloaded it >> from the pdb I removed all other water and ions - it just made pdb2gmx >> easier to work with. >> > > I simply hand-edited the .gro by making up two ions and put them > somewhere near the corners and added a short energy minimization. > Then, I added one line in the .top for the ions. > >> The 1080 scaled nicely with the 1080 ti, these are really nice pieces of >> hardware. and you are correct, given the choice of increased processors vs >> faster processors - choose the latter. I have the AMD OC to 4.0 GH and it >> runs the same model almost as fast as as 32 core AMD at 3.7 GHz. > > Your system is possibly too slow to saturate the 1080Ti at this small > system size. In a much larger system, the lead of the 1080 Ti over the > 1080 may possibly reach the theoretical expectation. > >> I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day >> in NPT. And yes, if you can send the pdb, top, and itps I’t would be >> interesting to compare the two AMDs. >> > > I did upload the stuff here + a readme-file. This system is much too > large for a single box + GPU (for productive runs), but maybe in 5 years > or so we can watch capillary waves through connected IMD/VMD in real- > time ;) > > => http://suwos.gibtsfei.net/d.dppc.4096.zip > > Regards > > Mirco > > -- > 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. -- 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.
Re: [gmx-users] REMD Plots
Hi Joel, Thank you very much. On Wed, Jan 9, 2019 at 3:27 PM Joel Awuah wrote: > Hi Shan, > I am not quite sure if you want to generate an REMD simulation mobility in > temperature space for the 30 replicas. If that be the case, then you can > use the data in the replica_temperature.xvg file to plot replica index vs > REMD steps. The 1st column in the file corresponds to the REMD steps and > 2nd to 31st correspond to the mobility of replicas 0 to 29. > > Hope this helps? > > cheers > Joel > > > On Wed, 9 Jan 2019 at 13:23, Shan Jayasinghe > > wrote: > > > Dear Gromacs users, > > > > How do we plot a graph for temperature vs swap step number using a REMD > > simulation with 30 systems. I already generated the replica_temp.xvg and > > replica_index.xvg files using demux.pl script. > > > > Thank you. > > > > Best Regards > > Shan Jayasinghe > > -- > > 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. > > > > > -- > Joel Baffour Awuah > PhD Candidate > *Institute for Frontier Materials* > > *Deakin University* > *Waurn Ponds, 3126 VIC* > *Australia +61450070635* > -- > 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. > -- Best Regards Shan Jayasinghe -- 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.
Re: [gmx-users] Results of villin headpiece with AMD 8 core
Hi Paul, thanks for your reply. On 11.01.2019 23:20, paul buscemi wrote: > Getting the ion and SOL concentration correct in the top is trickier ( for me > ) than it should have been, If you happen to reuse both solvate and > genion during the build keeping track of the top is like using a digital > rubics cube..! The charge the villin was +1 because after I downloaded it > from the pdb I removed all other water and ions - it just made pdb2gmx easier > to work with. > I simply hand-edited the .gro by making up two ions and put them somewhere near the corners and added a short energy minimization. Then, I added one line in the .top for the ions. > The 1080 scaled nicely with the 1080 ti, these are really nice pieces of > hardware. and you are correct, given the choice of increased processors vs > faster processors - choose the latter. I have the AMD OC to 4.0 GH and it > runs the same model almost as fast as as 32 core AMD at 3.7 GHz. Your system is possibly too slow to saturate the 1080Ti at this small system size. In a much larger system, the lead of the 1080 Ti over the 1080 may possibly reach the theoretical expectation. > I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day > in NPT. And yes, if you can send the pdb, top, and itps I’t would be > interesting to compare the two AMDs. > I did upload the stuff here + a readme-file. This system is much too large for a single box + GPU (for productive runs), but maybe in 5 years or so we can watch capillary waves through connected IMD/VMD in real- time ;) => http://suwos.gibtsfei.net/d.dppc.4096.zip Regards Mirco -- 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.
[gmx-users] Changing mdp options for a restart
http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart I tried to simulate instantaneous perturbation in topology and did everything as in instruction (below). Changing mdp options for a restart If you wish to make changes to your simulations settings other than length, then you should do so in the mdp file or topology, and then call gmx grompp -f possibly-changed.mdp -p possibly-changed.top -c state.cpt -o new.tpr gmx mdrun -s new.tpr -cpi state.cpt to instruct gmx grompp to copy the full-precision coordinates in the checkpoint file into the new tpr file. You should consider your choices for tinit , init-step , nsteps and simulation-part . You should generally not regenerate velocities with gen-vel , and generally select continuation so that constraints are not re-applied before the first integration step. My steps are: gmx grompp -f -p -c 4-daspi-S0.gro -o S0 ; old topology compilation gmx mdrun -v -deffnm S0 ; old run gmx grompp -f grompp-S1.mdp -p topol-S1.top -c S0.cpt -o S1 ; here begins actual part But I got error message from "gmx grompp, version 2019" Error in user input: Invalid command-line options In command-line option -c File name 'S0.cpt' cannot be used for this option. Only the following extensions are possible: .gro, .g96, .pdb, .brk, .ent, .esp, .tpr What is the reason of mistake, or something wrong in manual? -- 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.
[gmx-users] Single precision enough for MD of peptide?
Hi GMX users, I just installed GROMACS 2018.4 on my windows PC without GPU support. My PC is capable of only single precision with a 64-bit memory, would this affect the trajectory of my peptide? Many thanks, Neena -- 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.
