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
Received on Fri Jun 20 2014 - 03:30:02 PDT
