Of course, because I'm not right in the head, I would prefer defining a
local orthonormal coordinate system myself so one could do this arbitrarily
rather than strictly along the x, y, and z axes...
On Fri, Jun 20, 2014 at 9:13 AM, Scott Le Grand <varelse2005.gmail.com>
wrote:
> 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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>>
>
>
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Received on Fri Jun 20 2014 - 09:30:02 PDT
