Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-25 Thread Guillaume Chevrot
Dear Xavier, 2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? FYI, I tried 10 and 1 and the energy drift is exactly the same. Similar flags apply to temperature and pressure and I believe might seriously affect

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-25 Thread Michael Shirts
Hi, all- At this point, any fixes are going to be in the 5.0 version, where the integrators will be a bit different. If you upload your system files to redmine.gromacs.org (not just the .mdp), then I will make sure this gets tested there. On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-13 Thread Mark Abraham
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: 2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-12 Thread XAvier Periole
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Similar flags apply to temperature and pressure and I believe might seriously affect energy conservation. XAvier. On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote: Didn't see any problem in

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-12 Thread Guillaume Chevrot
2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-12 Thread Guillaume Chevrot
2013/10/12 XAvier Periole x.peri...@rug.nl Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one? Thanks for the suggestion. I'll try next week and I'll show the results ASAP. Guillaume Similar flags apply to temperature and pressure and I believe might seriously

[gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Guillaume Chevrot
Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Michael Shirts
Hi, Guillaume- No one can tell you if you did anything wrong if you didn't tell us what you did! There are literally thousands of combinations of options in running an NVE simulation, a substantial fraction of which are guaranteed not to conserve energy. If you post the files (inputs and

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Mark Abraham
On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Guillaume Chevrot
Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision /

Re: [gmx-users] energy drift - comparison of double and single precision

2013-10-11 Thread Mark Abraham
Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at

Re: [gmx-users] Energy Drift

2011-10-19 Thread Per Larsson
Hi Justin! Do you maybe have an example of such a protein (preferably not too large :-), that I could run some tests on? I'd be interested in seeing if there has been any bugs introduced in the cutoff code that destabilises proteins that way. Thanks /Per 18 okt 2011 kl. 23:41 skrev Justin A.

[gmx-users] Energy Drift

2011-10-18 Thread Ben Reynwar
I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much. The simulation is a protein of about 5000 atoms using GBSA, a time step of

Re: [gmx-users] Energy Drift

2011-10-18 Thread Justin A. Lemkul
Ben Reynwar wrote: I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much. The simulation is a protein of about 5000 atoms

[gmx-users] Energy Drift in Gromacs 4.0

2009-03-10 Thread Ilya Chorny
Hello All, I am trying to run some calibration calculations with 2/4 fs time steps. I am trying to reproduce the results in the Gromacs 4.0 paper on a protein/water (not the same protein) system with ~100K atoms. I ran 1 ns simulation in the NVE ensemble. My mdp params are shown below. Topolgy was