Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent

From: Ilyas Yildirim <>
Date: Fri, 30 Jan 2015 15:11:03 +0000 (GMT)

To MODERATOR: I've sent the same email today early morning with some
attachments, but the size of the attachments were too big, which required
the moderator to decide to post or not. I am re-sending the email without
the attachments; thus, please discard and do not send the previous email
to the list.

Dear Jason, Scott, Dave, and Ross,

I have been reading this thread since Rosie described the problem with the
energies coming out different at each new calculation. Scott and Jason were
talking about the problem arising due to the GB model, or the method it is
being used by cuda. So, I provided Rosie with a new prmtop/inpcrd input set
directly created with ff12SB force field. The new set seems to work fine. The
previous one was created with new frcmod/lib files loaded over ff12SB. The new
frcmod has new atom types in it, and it seems that those are the ones causing
the problem (though it is not clear yet to me why energies are different at the
end). You can check out the prmtop.notworking and prmtop.working from the
following address:

While creating the prmtop.notworking file, I used the following leap script to
create it.

---------- -----------
source leaprc.ff12SB
addPdbAtomMap {
   { "OP1" "O1P" } { "OP2" "O2P" }
   { "HO5'" "H5T" } { "HO3'" "H3T" }
   { "H5'" "H5'1" } { "H5''" "H5'2" }
   { "H2'" "H2'1" } { "H2''" "H2'2" }
addAtomTypes {
   { "DH" "H" "sp3" }
   { "C1" "C" "sp2" }
   { "C2" "C" "sp2" }
   { "C3" "C" "sp2" }
   { "C4" "C" "sp2" }
   { "C5" "C" "sp2" }
   { "C6" "C" "sp2" }
   { "C7" "C" "sp2" }
   { "C8" "C" "sp2" }
   { "CI" "C" "sp3" }
   { "OZ" "O" "sp3" }
loadamberparams ./libraries/frcmod.parmCHI
loadamberparams ./libraries/frcmod.ionsjc_tip3p
loadoff ./libraries/
loadoff ./libraries/ions08.lib
set default PBradii mbondi2
mol = loadpdb model.pdb
saveAmberParm mol prmtop.notworking inpcrd

If someone wants to use a GB model on a modified system (or let's say a model
with revised force field) I am not sure what else needs to be defined in the
leap input file. In the cuda version of pmemd, is there a specific file that
has info on the GB model which needs to be modified in order make sure
that the new atom types are recognized by AMBER 14 DPFP runs (so that the
GB model won't complain about it)? It seems that usage of new atoms types
somehow creates this whole problem. Thanks.

Best regards,

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry | University of Cambridge =
   = Lensfield Road (Room # 380) | Cambridge, UK CB2 1EW =
   = Ph.: +44-1223-336-353 | E-mail: =
   = Website: =
   = ------------------------------------------------------- =
   = =
   = =

On Thu, 29 Jan 2015, Jason Swails wrote:

> On Thu, Jan 29, 2015 at 9:14 PM, Scott Le Grand <>
> wrote:
>> Hey Jason, I found the root cause and checked in a fix.
>> If I put a printf into any CUDA kernel, that's the end of its performance.
>> Printf is a hog. It's only useful for debugging purposes.
> ‚ÄčThat's what I was suggesting it be used for. Basically what I was curious
> about was whether or not any of the GB tests in our test suite hit the code
> path where dr didn't get initialized. If it did, that would seem (to me)
> to be clear evidence that that code path is not illegal/unusual (i.e.,
> indicative of bad parameters). If that printf is never triggered during
> the test suite, the parameters may be unusual. I certainly wasn't
> suggesting it be left in permanently. I'll take a look if I have time.
>> The beginning
>> of this thread has links to the data to repro this behavior. It's weird
>> that we never saw this before.
>> Just initialializing PMEFloat dr does the trick. The bug is fixed.
> ‚ÄčI saw the commit log :).
> Thanks,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

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Received on Fri Jan 30 2015 - 07:30:03 PST
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