[gmx-users] soft-core and coulomb transformation

Berk Hess gmx3 at hotmail.com
Mon Nov 12 18:09:12 CET 2007 

Hi,

I am afraid you might be right.

I thought I had fixed all checks when implementing free energy for PME.
But it seems that the splines are only constructed for particles with 
non-zero
A charges.
If this is the (only) problem, it can easily be checked by replacing
in pme.c in spread_on_grid both lines:
if (!bHaveSplines) {
by
if (TRUE) {

If this is the problem, I will fix it, but then (probably) still retaining
the optimization of using the B-splines only once.

I guess normally one would choose the B-state to be the zero state.
But for mutation studies this bug (if it is really the problem) could
give small errors that one might not notice directly...

Berk.


>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
>CC: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] soft-core and coulomb transformation
>Date: Mon, 12 Nov 2007 08:45:33 -0800
>
>Hi, Bharat, and David vdS.
>
>This indeed is looking suspiciously like a real problem. FWIW, I did
>reproduce your original problem using my own input files and PME with
>gromacs 3.3.1.
>
>It's still a bit perplexing, in that you seem to be getting basically
>the "right" answers for the forward transformation (at least, by
>comparing the PME forward results with the cutoff forward results) but
>the reverse transformation is crazily wrong. I'm having a hard time
>figuring out what sort of bug could cause this to happen.
>
>The only thing I can come up with so far that might cause this is a
>bug in the handling of B state 1-4 interactions with PME. Since
>methane has no B state 1-4 electrostatic interactions, the
>ethane->methane transformation would be OK both with and without PME.
>But methane->ethane would go awry with PME because ethane still has
>1-4 electrostatic interactions.
>
>If I remember correctly, though, you reported that the vacuum
>calculations work fine? That wouldn't be consistent with my
>explanation above, and perhaps would suggest that the problem is
>interactions with water, somehow?
>
>Just speculation at this point.
>
>I'm doing some more testing on this end (trying to come up with a more
>minimal example). I'm checking to see whether discharging phenol in
>water gives the same results as charging phenol in water.
>
>David
>
>
>On 11/11/07, bharat v. adkar <bharat at sscu.iisc.ernet.in> 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.
> >
> >
> > bharat
> >
> >
> >
> >
> >
> > >
> > > David
> > >
> > >
> > > Hope that helps. Keep me posted on what you find.
> > >
> > > On Nov 7, 2007 10:42 PM, bharat v. adkar <bharat at sscu.iisc.ernet.in> 
>wrote:
> > >>
> > >> Hi David,
> > >>
> > >> This is regarding our discussion on gromacs mailing list on 
>"soft-core
> > >> and coulomb transformation". Sorry for delay in reply. I am  
>attaching a
> > >> TGZ file which contains a script to run the simulations and a MDP 
>folder
> > >> with all required files.
> > >>
> > >> The system is Ace-Ala-Nac, i.e., alanine capped at both ends.
> > >>
> > >> The MDP files are made to run the FORWARD simulations, i.e., from
> > >> alanine->glycine. To run the REVERSE simulations, in all MDP files,
> > >> "define = -DFE_coul_rev" has to be defined.
> > >>
> > >> I am sorry for a lot of botherance. but i am not getting the same 
>values,
> > >> within error limit, as i mentioned in the mailing list. I will send 
>my set
> > >> of values to you most probably by tomorrow.
> > >>
> > >> Thanks.
> > >>
> > >> bharat
> > >>
> > >> --
> > >> This message has been scanned for viruses and
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> > >> believed to be clean.
> > >>
> > >>
> > >
> > >
> >
> > --
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> >
> >
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