Re: [AMBER] NVE GPU question

From: Ross Walker <>
Date: Thu, 22 Jan 2015 10:48:28 -0800

Hi Joe,

I've moving this over to the AMBER mailing list as I think this is of interest to others and they maybe able to offer more suggestions than me.

My initial guess is that this may be due to the way PME is working with ionic liquids. Are the systems definitely neutral in all cases? The behavior of PME maybe different if the system is not neutral.

My second suspicion is that the average velocities might be higher for ionic liquids - have you tried at different temperatures. In the case of a protein in TIP3P water with Shake you have no atoms that are affectively unconnected to anything else. So your waters have an effective mass of 18 per molecule and your protein has a huge per molecule mass. The waters are less than sodium for example in mass but there may be hydrogen bonding effects, or their VDW are different such that they are moving less. This is just a stream of conciousness - I am not sure why you'd see the difference but I could image there being more effective loss of precision somewhere due to either - charge charge interaction being larger on average - bigger +'ve and -'ve numbers that cancel out for example. This sort of thing would certainly effect energy conservation within the SPFP precision model.

There might also be more integration error going on if the particles are moving faster although that would imply a higher overall temperature. Does reducing the timestep help?

Have you tried DPFP to see how it does with that?

Anyone else want to chime in?

All the best

> On Jan 20, 2015, at 3:26 PM, Joseph Baker <> wrote:
> Hi Ross,
> I hope you've been doing well. I've got a question for you in relation to trying to compare some energy drifts to your paper on explicit solvent PME in GPU amber. My protein simulations have NVE drift that is spot on (5 x 10^-6 kT/ns/dof for 1 fs steps, and 1.3 x 10^-5 kT/ns/dof for 2 fs step), so that's been very nice (the code really does great for energy conservation in the protein NVE sims).
> However, I've tried to dabble a bit with some ionic liquids (currently am testing the one that is in the amber ionic liquid tutorial that uses gaff parameters). There I've tried a whole ton of different timestep, cutoff, equilibration protocol combinations, and the best I can seem to get is around a couple x 10^-4 kT/ns/dof (these are pure ionic liquid simulations, but I get a similar result in a simulation where I sprinkled the ionic liquid inside a box of water, actually there I get a bit worse, about 10^-3 kT/ns/dof). I realize that this is still not very large at all, but do you have any reason to believe that pmemd.cuda with ionic liquids is going to do worse in NVE?
> If you've got a spare minute at some point for an opinion on this, it would be appreciated!
> Thanks,
> Joe
> --
> Joseph Baker, PhD
> Assistant Professor
> Department of Chemistry
> C101 Science Complex
> The College of New Jersey
> Ewing, NJ 08628
> Phone:(609) 771-3173 <tel:%28609%29%20771-3173>
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Received on Thu Jan 22 2015 - 11:00:03 PST
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