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

On Thu, Jan 22, 2015 at 8:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Jan 22, 2015 at 8:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Jan 22, 2015 at 8:09 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark Thank you for your patient reply. I've tried using the

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

On Thu, Jan 22, 2015 at 10:08 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark, I've reproduced runs that have different initial velocities and also different setups, e.g. different kinds of NPs. The force field is MARTINI coarse-grained force field with polarizable water. OK, that's great -

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

Hi Mark Thank you for your patient reply. I've tried using the exact same set up (rcoulombic =3.258 fourierspacing = 0.325, rlist =1.4, rlistlong =3.258, rvdw=1.2) as the auto-tune of would have changed the parameters to, and still it won't reproduce the result obtained by auto-tune, just

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

On Thu, Jan 22, 2015 at 8:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Jan 22, 2015 at 8:09 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark Thank you for your patient reply. I've tried using the exact same set up (rcoulombic =3.258 fourierspacing = 0.325, rlist =1.4, rlistlong

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

On Thu, Jan 22, 2015 at 8:09 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark Thank you for your patient reply. I've tried using the exact same set up (rcoulombic =3.258 fourierspacing = 0.325, rlist =1.4, rlistlong =3.258, rvdw=1.2) as the auto-tune of would have changed the parameters to, and

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

Hi Mark, I've reproduced runs that have different initial velocities and also different setups, e.g. different kinds of NPs. The force field is MARTINI coarse-grained force field with polarizable water. The compression of lipid bilayer might because of the particular simulation setup in my

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

Hi Mark, Thanks for reply. I put the md.log files in the following link https://www.dropbox.com/sh/d1d2fbwreizr974/AABYhSRU03nmijbTIXKKr-rra?dl=0 There are four log files 1.GMX 4.6.5 -tunepme (the coulombic cutoff is tuned to 3.253) 2.GMX 4.6.5 -notunepme rcoulomb= 3.3 , fourierspace = 0.33

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

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 interested is to manually reproduce the result that tune_pme give me in the first case using

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

Not (all) directly related, but a few comments/questions: - Have you tried 4.6.7 or 5.0.4? - Have you considered using the Verlet scheme instead of doing manual buffering? - lincs-order=8 is very large for 2fs production runs - typically 4 is used. - Your fourier spacing is a lot (~25%) finer

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

On Tue, Jan 20, 2015 at 9:18 PM, Jiaqi Lin jq...@mit.edu wrote: Hi Mark, Thanks for reply. I put the md.log files in the following link https://www.dropbox.com/sh/d1d2fbwreizr974/AABYhSRU03nmijbTIXKKr-rra?dl=0 There are four log files 1.GMX 4.6.5 -tunepme (the coulombic cutoff is tuned

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

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 to ~3.3

[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

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 to ~3.3 nm (stated in md.log) when I set -npme to be 28 (128 total CPU