Looking at the rest of the surrounding code, I *think* this works because
the three axes are independent and additive components (if this were
otherwise, Ross is dead-on about breaking detailed balance). They just
happen to have the same weight according to the rules we specify.
That said, of course validate it with some NVE runs...
And then if this were actually something people needed, I would formally
add a constraint type with per axis components rather than kludge the code
like this...
On Fri, Jun 20, 2014 at 8:57 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Pierpaolo
>
> ---
> I modified the file constraints.F90 in /usr/local/amber14/src/pmemd/src as
> follows
>
> wt = weit(j) # line 245
> ax = x(1, i) - xc(1, i)
> ay = x(2, i) - xc(2, i)
> az = x(3, i) - xc(3, i)
> wx = 0.d0 # here I changed the values of wx and wy
> wy = 0.d0 #
> wz = wt * az
>
> ---
>
> Have you worked through the math for this to make sure it is valid and
> obeys detailed balance? I haven't had a chance to myself but I cannot
> believe that one can simply zero the constraint here and not do anything
> with regards to balancing the gradients etc. If you run your simulation
> with NVE does it conserve energy with this modification? If not then you
> can't simply make such a change. Even if it appears to run stably all of
> your statistical distributions will come out incorrect.
>
> You need to work through the math first and verify this is correct before
> simply making edits in the code.
>
> All the best
> Ross
>
>
>
> On 6/20/14, 3:26 AM, "Pierpaolo Cacciotto"
> <pierpaolo.cacciotto.dsf.unica.it> wrote:
>
> >Dear Ben,
> >
> >yes that's the only change I made in the code and I can say that, at least
> >for my system, it is working.
> >
> >About my system, I should say that is an in-vacuo equilibration of a
> >protein inserted in a pre-equilibrated POPE membrane.
> >After the insertion there were gaps between protein and membrane so that I
> >could not add water molecules "safely".
> >Therefore I needed to equilibrate the system in-vacuo before adding water
> >but without this change in the code the system didn't equilibrate well (in
> >particular, the membrane thickness changed). Now, with this change it
> >seems fine to me.
> >
> >
> >Regards,
> >Pierpaolo
> >
> >
> >
> >
> >> .Ylenia: The only option that is currently supported in Amber is to use
> >> distance restraints like in umbrella sampling. Note that group
> >>restraints
> >> are currently not available in the GPU-accelerated pmemd.cuda code, so
> >>you
> >> are limited to pmemd and pmemd.MPI.
> >>
> >> .Brian: It is correct that SHAKE is only available for hydrogen bonds
> >>or a
> >> set of bonds between atoms. It is currently not possible to constrain
> >> molecules or groups of molecules with SHAKE.
> >>
> >> .Pierpaolo: Is that all that you changed in the source code? I think
> >>this
> >> should be added as an official option to Amber so that any combination
> >>of
> >> X Y Z restraints can be selected.
> >>
> >> All the best,
> >> Ben Madej
> >> UCSD Chemistry and Biochemistry
> >> SDSC
> >> ________________________________________
> >> From: Pierpaolo Cacciotto [pierpaolo.cacciotto.dsf.unica.it]
> >> Sent: Wednesday, June 18, 2014 10:03 AM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Setting up z-constraint
> >>
> >> Dear Ylenia,
> >>
> >> I had almost the same problem and I partially solved it for the pmemd
> >>cpu
> >> version in the following way:
> >>http://archive.ambermd.org/201405/0596.html
> >> (The changes in the link are now working...I just made some mistakes
> >> recompiling the program).
> >>
> >> Regards,
> >> Pierpaolo
> >>
> >>
> >>
> >>> Dear amber users,
> >>>
> >>> I need help setting up my MD simulation.
> >>> Basically I want to constraint my molecule on the z axis (specific
> >>>depth
> >>> in
> >>> a phospholipid membrane) and leave it free to move in the x and y
> >>> planes.
> >>>
> >>> Any suggestion will be greatly appreciated!!
> >>>
> >>> Ylenia
> >>>
> >>> --
> >>> *Ylenia Cau, PhD Student*
> >>> *Department of Biotechnology, chemistry and pharmaceutical sciences, *
> >>> *University of Siena, Via a Moro 2, 53100 Siena, Italy*
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>
> >>
> >> --
> >> Pierpaolo Cacciotto - PhD Student
> >> Department of Physics
> >> University of Cagliari
> >>
> >> Cittadella Universitaria
> >> 09042 Monserrato - Italy
> >>
> >> Phone: +39 070 675 4839
> >> E-mail: pierpaolo.cacciotto.dsf.unica.it
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> >--
> >Pierpaolo Cacciotto - PhD Student
> >Department of Physics
> >University of Cagliari
> >
> >Cittadella Universitaria
> >09042 Monserrato - Italy
> >
> >Phone: +39 070 675 4839
> >E-mail: pierpaolo.cacciotto.dsf.unica.it
> >
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 20 2014 - 09:30:02 PDT
