[gmx-users] soft-core and coulomb transformation

[David van der Spoel]

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se