bharat v. adkar wrote:
Hi David,
I am keeping the subject same so that it is helpful to track in
future.... :)
On Sat, 10 Nov 2007, David Mobley wrote:
Dear Bharat,
OK, I went ahead and ran with your topologies using my own run
scripts. My runs haven't finished yet, but looking at just
<dV/dlambda> values from equilibration, I seem to be seeing roughly
the same trends you do. In particular:
(1) The forward simulation always gives dv/dlambda values that are
fairly close to -2 at each lambda
(2) The reverse simulation gives a range of <dv/dlambda> values at
different lambda values, and switches from positive to negative as
lambda increases.
The integral of <dV/dlambda> in the forward case is NOT the negative
of the integral of <dV/dlambda> for the reverse case, which is what it
should be.
Obviously, something is wrong here, and it doesn't seem to be your run
input files. I don't see anything obviously wrong with your topology
files, either -- as far as I can tell your charge groups are OK.
My suggestion is to try to strip this down to a simpler case where it
will become more clear what the problem is. Maybe ethane->methane
rather than with the capping on the ends. (Did you say you have the
same problem with ethane->methane? It would be easier to troubleshoot
those topologies).
As I mentioned earlier, ethane to methane transformation also shows the
same behaviour. I am almost sure that the topologies and other input
files are correct. I am pasting below the output of the
coulomb-transformation for both, ethane to methane (forward) and methane
to ethane (reverse). Topology is the same as i mentioned few mails back...
Forward charge transformation
lmbd dg/dl error
0.00 -8.286304 0.0108319
0.05 -8.32708 0.0114018
0.10 -8.328157 0.0095819
0.15 -8.344236 0.00893341
0.25 -8.353463 0.00984712
0.40 -8.368163 0.0104302
0.50 -8.397035 0.00969758
0.60 -8.415603 0.00908416
0.75 -8.448185 0.00941215
0.85 -8.484247 0.00922024
0.90 -8.481465 0.00885981
0.95 -8.495802 0.00961897
1.00 -8.501283 0.00957299
Reverse charge transformation
0.00 13.770658 0.074592
0.05 13.331217 0.0778554
0.10 13.075527 0.0722786
0.15 12.483814 0.0750718
0.25 11.789282 0.0674654
0.40 10.730386 0.0875609
0.50 10.008684 0.0807128
0.60 9.266026 0.0736956
0.75 7.999017 0.0738001
0.85 7.388243 0.0832792
0.90 6.991334 0.0828869
0.95 6.595921 0.0796503
1.00 6.180366 0.0893983
As can be clearly seen, both transformations are not equivalent. (These
are output from the 1 ns simulations.)
If you get to the point where you're convinced it has nothing to do
with your topology, you could submit a bugzilla -- but it would be a
good idea to be more sure that there is no problem with your topology,
first. Also it would be helpful to have more evidence about where the
bug might be, if there is one (hence the importance of stripping this
down to the "minimum" topology necessary to reproduce the problem).
You might also, for example, just try turning off the charges on
methane in water. You could also try turning on the charges in methane
in water. These two should be equivalent (except for the sign) of
course.
Keep me posted on what you find out.
to further see what happens, i used cut-off instead of pme and that
seems to be giving okay results. i tried running only 20 ps runs as in
equilibration, and there the values look as per expectations. then tried
with Ace-Ala-Nac <-> Ace-Gly-Nac also. both seems okay. below are the
values i obtained:
Ethane <-> Methane
forward
0.00 -8.277302 0.0747561
0.05 -8.346413 0.105338
0.10 -8.311737 0.0775508
0.15 -8.326182 0.0749244
0.25 -8.383022 0.0741275
0.40 -8.309543 0.199901
0.50 -8.388351 0.0807475
0.60 -8.334778 0.0769525
0.75 -8.444722 0.0556352
0.85 -8.541355 0.0529021
0.90 -8.562161 0.079475
0.95 -8.588182 0.0679287
1.00 -8.535591 0.0505447
reverse
0.00 8.647486 0.0848346
0.05 8.571583 0.0678888
0.10 8.410289 0.04688
0.15 8.336588 0.085721
0.25 8.536206 0.0457025
0.40 8.452587 0.0730119
0.50 8.397571 0.0540216
0.60 8.379067 0.0775835
0.75 8.345908 0.0889559
0.85 8.408099 0.082048
0.90 8.284268 0.0632315
0.95 8.1428 0.123793
1.00 8.303987 0.0505205
and for Ace-Ala-Nac <-> Ace-Gly-Nac
forward
0.00 -2.113457 0.160573
0.05 -2.056746 0.0790143
0.10 -2.619748 0.242052
0.15 -2.470358 0.247365
0.25 -2.121426 0.623961
0.35 -2.210045 0.0567349
0.45 -2.173477 0.0483762
0.50 -2.156053 0.167631
0.55 -2.156565 0.0948302
0.65 -2.194102 0.0810602
0.75 -2.302156 0.306185
0.85 -2.28119 0.0545011
0.90 -1.936869 0.147152
0.95 -2.275215 0.190621
1.00 -2.221756 0.124669
reverse
0.00 2.30627 0.169452
0.05 2.102584 0.181941
0.10 2.531891 0.27292
0.15 2.491334 0.200524
0.25 2.020721 0.0577124
0.35 2.42911 0.133624
0.45 2.113785 0.24776
0.50 2.312891 0.056794
0.55 2.147666 0.0652882
0.65 2.259201 0.0969329
0.75 2.341642 0.0767809
0.85 2.381157 0.19062
0.90 2.293333 0.238674
0.95 2.197692 0.175085
1.00 1.921228 0.0853432
in both the cases, the values do not change much, but they appear to be
satisfying.
So everythings approximately zeroes down to the suspision that PME
implementation for TI is buggy.
Developers, please have a look at and confirm.
please submit a bugzilla with all input files and these output results
please add information about your GROMACS installation as well.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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