Re: [gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

/2015 7:18 PM, Mark Abraham wrote: On Tue, Jan 20, 2015 at 11:48 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Szilard, - I've tired 5.0.1 and it gives the same result. So 4.6.7 or 5.0.4 is better, but in what way? - I've tired Verlet scheme and it gives small change of cutoff and grid. But what I really

Re: [gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

in normal simulation setup (-notunepme, Verlet). That means I have to redo all the simulations, and that is a huge amount of work. I'll try to do the test as you suggested and see if it is a bug. Thank you Jiaqi On 1/22/2015 2:34 PM, Mark Abraham wrote: On Thu, Jan 22, 2015 at 8:09 PM, Jiaqi Lin jq

Re: [gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

Abraham wrote: On Thu, Jan 15, 2015 at 3:21 AM, Jiaqi Lin jq...@mit.edu wrote: Dear GMX developers, I've encounter a problem in GROMACS concerning the auto-tuning feature of PME that bugged me for months. As stated in the title, the auto-tuning feature of mdrun changed my coulomb cutoff from 1.4 nm

Re: [gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

after the PP-PME load balancing. Even if you want to stick to these parameters, you should tune the rank split (manually or with tune_pme). - The above contributes to the high neighbor search cost too. -- Szilárd On Tue, Jan 20, 2015 at 9:18 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark, Thanks

[gmx-users] how does PME auto-tuning work

Dear GROMACS users and developers, In GMX 4.6 or up, 'mdrun' can automatically adjust direct and reciprocal part of PME calculation to boost up speed. But how does it actually implemented in the code? I tried to manually set PME cutoff and fourierspacing but get different result. Can

[gmx-users] how does PME auto-tuning work

Dear GROMACS developers, In GMX 4.6 or up, 'mdrun' can automatically adjust direct and reciprocal part of PME calculation to boost up speed. But how does it actually implemented in the code? I tried to manually set PME cutoff and fourierspacing but get different result. Can someone explain

[gmx-users] how does PME auto-tuning work

Dear GROMACS users and developers, In GMX 4.6 or up, 'mdrun' can automatically adjust direct and reciprocal part of PME calculation to boost up speed. But how does it actually implemented in the code? I tried to manually set PME cutoff and fourierspacing but get different result. Can

[gmx-users] how does PME auto-tuning work

Dear GROMACS developers, In GMX 4.6 or up, 'mdrun' can automatically adjust direct and reciprocal part of PME calculation to boost up speed. But how does it actually implemented in the code? I tried to manually set PME cutoff and fourierspacing but get different result. Can someone explain

[gmx-users] how does PME auto-tuning work

someone explain how does PME auto-tuning work in the code? Thanks Best Jiaqi -- Jiaqi Lin postdoc fellow The Langer Lab -- 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

[gmx-users] results produced by auto-tuning of Coulomb cut-off/grid for PME can not be reproduced by manually setting the Coulomb cut-off and grid spacing

. PotentialKinetic En. Total Energy Temperature 6.20627e+04 -1.61205e+074.34624e+06 -1.17743e+07 3.00659e+02 Pressure (bar) Constr. rmsd 2.13582e+001.74243e-04 Best Jiaqi -- Jiaqi Lin postdoc fellow The Langer Lab -- Gromacs Users mailing list * Please search