Re: amber-developers: ptraj precision

From: Carlos Simmerling <>
Date: Tue, 06 Feb 2007 09:16:45 -0500

Hi Bob,
I'm not sure why you say I'm not correct. All I said was that
my fortran program has no problem reproducing the values, so
in my opinion it must be a problem with ptraj. What I wanted was
the "same" numbers in the file, some of the things you mention
below are interesting but not really relevant to my issue of
the values in the restart and traj just being different. With
my (double precision) fotran program, I get the same coordinates
in restart or traj and the same energies (yes, to within the output
of sander). With ptraj that didn't happen. I wasn't talking about
doing an "exact" restart, which of course we can't do with either
traj or restart files in non-binary. The point is that ptraj does
not properly write out what is in the coordinate file that it
reads, and that should get fixed.
thanks for your help with this!

Robert Duke wrote:
> Hi Carlos -
> You are not correct; the conversion error seen here is due to using a
> float as the input variable, as well as a float reading format, but
> there would still be no error associated with that if there were not
> unavoidable problems with the mix of internal and external
> representation. The reason you don't "see" any conversion error is
> that using double precision in fortran, the conversion error occurs
> down around decimal place 16-17 (if memory serves). SO you WOULD see
> differences in a restart trajectory, but once again you may have to do
> something like a debug dump of the energies to actually notice it due
> to truncation of mdout output. The reason I am being sticky about
> this point is that you were talking about "exact conversion to
> restart"; the only way to get this is with a binary restart file which
> I am not sure we reliably support (I know there are input options to
> do this; I have no confidence that the stuff actually works across all
> platforms, having seen the standard fortran binary i/o fall on it's
> face before - the specification of external (file) representation is
> incomplete and vendor specific). We should maybe extend NetCDF to
> cover the restrt and inpcrd files sometime, if folks really want to be
> able to do an "exact" restrart.
> Regards - Bob
> ----- Original Message ----- From: "Carlos Simmerling"
> <>
> To: <>
> Sent: Tuesday, February 06, 2007 7:44 AM
> Subject: Re: amber-developers: ptraj precision
>> I should point out that I wrote a simple fortran program to write
>> restarts
>> and I get exactly what I expected- the number in the traj file followed
>> by zeroes. So, I don't think it is a problem with internal
>> representation,
>> it's something with either ptraj or C.
>> carlos
>> Robert Duke wrote:
>>> Carlos -
>>> I expect the problem is internal binary representation of the
>>> floating point numbers. So the input trajectory file values may not
>>> be exactly representable, though you are probably coming closer
>>> internally to your input than it appears in your restart output
>>> (which also suffers from not exactly representing the internal
>>> value). The only way to avoid this sort of thing is with BCD -
>>> binary-coded decimal, which I believe is probably available in Cobol
>>> and assembler :-) (probably PL/1 too).
>>> Regards - Bob
>>> ----- Original Message ----- From: "Carlos Simmerling"
>>> <>
>>> To: <>
>>> Sent: Monday, February 05, 2007 5:18 PM
>>> Subject: amber-developers: ptraj precision
>>>> I am reading a trajectory file into ptraj and writing as restart,
>>>> with no actions (no imaging, etc).
>>>> I don't get quite what is in the traj file, does anyone know why?
>>>> The precision error is enough to affect the energies
>>>> and I want the actual coordinates from the traj file, not ones that
>>>> are +/- 0.000005 etc.
>>>> yes, I know that the ones in the traj file aren't exactly what was
>>>> in the original MD, but the point is to do an exact
>>>> conversion to restart.
>>>> thanks
>>>> carlos
>>>> input trajectory file:
>>>> 18.438 29.157 33.019 18.614 28.133 32.690
>>>> output restart from ptraj:
>>>> 18.4379997 29.1569996 33.0190010 18.6140003 28.1329994 32.6899986
>>>> --
>>>> ===================================================================
>>>> Carlos L. Simmerling, Ph.D.
>>>> Associate Professor Phone: (631) 632-1336
>>>> Center for Structural Biology Fax: (631) 632-1555
>>>> CMM Bldg, Room G80
>>>> Stony Brook University E-mail:
>>>> Stony Brook, NY 11794-5115
>>>> ===================================================================
Received on Wed Feb 07 2007 - 06:07:36 PST
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