Thanks Mark and Patrick for your prompt feedback.
I did look at hydration energies of small molecules and had no problem
reproducing the literature data. That being said, i noticed recently that
all was not well in some runs. I don't think it is a bug. I am more
inclined to think that it is a compilation problem.
Let me expand a little bit on the problem i'm experiencing with my
binaries.
The problem is as follows: using g_analyze_d, the average of block averages
is not the same as the same as the overall average. Getting a data average
should be easy enough, but it is not the case here.
Here is an example (see Details below):
from 0 to 1000ps ->g_analyze_d average is 1.634425e+03
from 1000 to 2000ps -> g_analyze_d average is 1.634059e+03
from 0 to 2000ps -> g_analyze_d average is 1.637816e+03 ---> a difference
of ~ 3kJ/mol compared with the 1ns blocks
from 2000 to 4000 ps > g_analyze_d average is 1.637791e+03
from 0 to 4000ps -> g_analyze_d average is 1.620341e+03 --> a difference of
~ 17kJ/mol compared with the 2ns blocks
The difference in averages is about 3 kJ/mol for ~ 1million data points (2
blocks of 1000ps vs 1 block of 2000ps, dt=0.002) and 14-17 kJ/mol for ~2
million data points (2 blocks of 2000ps vs 1 block of 4000ps, dt=0.002 ).
This is much greater than the double counting of the 1000ps or 2000ps data
point would contribute.
Also, if i process xvg files with some of my own scripts/programs (perl or
double-precision fortran), i get:
from 0->4000ps -> average is 1634.2
Also, if i trim the xvg file (using grep '^\..000') to retain data points on
every other 0.1 ps or so, g_analyze_d gives an average of 1.634125e+03 over
the 4000ps run, which looks like the right answer this time.
This is all very perplexing.
Thanks
Philippe
-----Details----
$GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -e 2000
Read 1 sets of 1000001 points, dt = 0.002
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.637816e+03 3.406546e+01 3.406546e-02 -0.168 -0.012
$GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -b 2000 -e 4000
Read 1 sets of 1000001 points, dt = 0.002
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.637791e+03 3.383955e+01 3.383955e-02 -0.154 -0.007
$GROMACS/bin/g_analyze_d -f prod-path.6.coul.l0.5.sol.xvg -e 4000
Read 1 sets of 2000001 points, dt = 0.002
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.620341e+03 3.649526e+01 2.580605e-02 0.676 0.008
---Details end----
On 6/22/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Hi all
>
> I have a silly problem and would welcome any suggestions. At this point
i
> suspect that this is a installation or compliation problem.
>
> First, let me say that i am a very unsophiticated user of gromacs.
> Please,
> bear with me if there is a well known fix for this.
> I have installed gromacs following the instructions on the website
> (settings
> for double precision and mpi). I started using it and everything seems
to
> work pretty well and I have run a number of jobs, mostly FEP's to
> familiarize myself better with Gromacs. The results i get are in line
> with
> published results. However, on some runs, the average dg/dl values i
get
> from the outputfile or from using g_analyze_d are out-of-line with what
i
> can obtain if i process the data myself. For example, i get a very
> different average values for 2 block-averages of 1ns each compared to
the
> average over the same 2ns. I've tried a few things and it looks like
the
> problem resides with my gromacs binaries. I can expand on this, if need
> be.
In the absence of a detailed description of what you're doing, it's going
to be hard to convince anyone that the problem resides with GROMACS rather
than your use of it, or your other method you refer to - particularly as
an inexperienced user. I'd suggest developing scripts that do an entire
calculation so that you have some basis for recording exactly what you did
and making it reproducible.
> Before I try reinstalling gromacs, i would appreciate getting some
> feedback
> on the key settings for a porper gromacs installation and how to check
for
> potential problems.
> Also, is there a set of test-jobs i can run to convince myself that i
> installed gromacs properly and that everything is working properly?
The installation guide on the website is fine for the vast majority of
systems. I'm not aware of a test suite per se, because MD is not
reproducible between slightly different hardware. You should be able to
reproduce ensemble averages with accuracy, however.
Mark
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