Hi all,
I just wanted to follow up on this issue to the list. The problem was
not reproducible by others, and was resolved for me when I compiled a
more recent checkout on my machine. So it would seem to be something
mysterious about that compilation that need not concern other AMBER users.
Thanks for all the suggestions and help.
-Hugh Heldenbrand
On 01/28/2010 12:03 PM, Hugh Heldenbrand wrote:
> I have two different versions of the AMBER 11 code that are giving me
> different results with the same input files.
>
> Here is what I have:
>
> My "older AMBER 11" is a CVS checkout from February 22nd, 2009. It
> was compiled with the Intel compiler version 9.1, version 9.0 of the
> Intel MKL libraries and version 1.2.2 of Open MPI.
>
> My "newer AMBER 11" is a CVS checkout from the middle of November,
> 2009. It was compiled with the Intel compiler version version 11.0,
> version 10.2.1.017 of the Intel MKL libraries and version 1.3.2 of
> Open MPI.
>
> I am doing some TI's on nucleobases in solution to determine their
> pKa's (so that I can later determine pKa shifts between the solution
> phase and the environment of my system).
>
> I discovered the problem when I tried to do some additional windows
> (additional values of lambda) using the newer code for a TI
> calculation that I had already done using the older code. The
> simulations using the newer code were not stable: I was getting the
> error message that vlimit was being exceeded. When I looked at the
> trajectory I saw that an amino group on my nucleobase was starting to
> flail around spontaneously after about 20 ps (by spontaneously I mean
> that I could not see anything colliding with the amino group, the
> hydrogens just started jumping around).
>
> Here are the endpoints of the TI that was unstable:
> lambda = 0: 9-methyladenine
> lambda = 1: 9-methyladenine with a hydrogen van der Waals radius at
> the N1 position, also the atom types of N1 and the exocyclic amine
> nitrogen were changed to give them new van der Waals radii.
>
> The van der Waals radius at the N1 was added using soft core
> potentials. The instabilities get worse (vlimit is exceeded earlier
> in the simulation) as lambda gets closer to 1.
>
> It seemed strange that only one of my nucleobases would be unstable,
> so I tried redoing some of my other older nucleobase calculations with
> the newer code. I do see differences in energy between the newer code
> and older code. In one case, the simulations produced the same output
> for the first 1500 fs or so, then I started to see differences in
> energy in the fourth decimal place. By 70 ps, the newer code energy
> is -8211 and the older code energy is -8260.
>
> I am using Langevin dynamics (using the same random number seed to
> compare the older and newer codes), so I wonder if that isn't masking
> small instabilities in my other nucleobase simulations using the newer
> code.
>
> So, have there been any changes to the TI code that might be causing
> this problem? I won't clutter up the listserv with parameter and
> input files, but I would be happy to send them to anyone who would
> like to try to reproduce this or examine them.
>
> -Hugh Heldenbrand
> Graduate Student,
> Chemistry Dept.
> University of Minnesota
>
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Received on Sat Jan 30 2010 - 07:30:03 PST
