Hi!!
No, selective aMD is not supported at this moment, we are working on it.
We have some code but have not tested it and merged it to the main amber
branch. We hope we can finish it and add it for the next release, but for
now you'll have to modify the code on your own if you really want to go
that way.
We have a person in our lab working on a protein inserted into a lipid
bilayer and regular aMD seems to be working fine for him.
Hope this helps,
Romelia
> Interesting question.
>
> I won't attempt to think about the modeling/chemistry/sampling
> ramifications...
>
> Computationally, if you look at sander's amd.F90 module, it could be the
> case that you could change the boosting loop over all atoms in the
> calculate_amd_total_weights routine which I copied in below.... so that
> it just looped over the atoms in the protein. I marked the loop below
> with <<<<<<<<<<<<<<<<<
>
> However, the preceeding calculations of "tboost" (torsion boost) appears
> very much based on the gross total of ALL dihedtrals. Splitting
> calculation of tboost between protein and membrane, at my first glance,
> is much tougher than carving out a subset of atoms to be boosted.
>
> I close by noting that I know little about which I write :) - and look
> forward with you to the advice of the AMD pros!
>
> subroutine
> calculate_amd_total_weights(atm_cnt,tot_potenergy,totdih_ene,frc,temp0)
>
> use constants, only: KB
> implicit none
> # include "parallel.h"
>
> ! Formal arguments:
> integer :: atm_cnt
> _REAL_ :: tot_potenergy
> _REAL_ :: totdih_ene
> _REAL_ :: frc(*)
> _REAL_ :: temp0
>
> integer :: i
>
> !AMD DUAL BOOST CALC START
> if(iamd.gt.0)then
> totalenergy = 0.0d0
> tboostall = 0.0d0
> fwgt = 1.0d0
> totalenergy = tot_potenergy + (tboost*temp0*KB)
> if (((iamd == 1).or.(iamd == 3)) .and. (totalenergy.le.EthreshP))
> then
> if (num_amd_lag .eq. 0) then
> tboostall = ((EthreshP - totalenergy)**2)/ &
> ((alphaP + (EthreshP - totalenergy))*temp0*KB)
> fwgt = (alphaP**2)/((alphaP + EthreshP - totalenergy)**2)
>
> do i = 1, atm_cnt <<<<<<<<<<<<<<<<<
> frc(i*3 - 2) = frc(i*3 - 2)*fwgt
> frc(i*3 - 1) = frc(i*3 - 1)*fwgt
> frc(i*3) = frc(i*3)*fwgt
> enddo
> end if
>
>
> On 06/16/2013 11:43 AM, Thomas Evangelidis wrote:
>> Dear AMBER list,
>>
>> Does AMBER12 support selective aMD? Can I apply the dihedral energy
>> boost
>> potential just on the torsion angles of the protein in a
>> membrane-protein
>> simulation?
>>
>> thanks,
>> Thomas
>>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Tue Jun 18 2013 - 11:30:02 PDT
