It's possible to make it more specific by using addljtype with a mask to
move the surface atoms to a new matrix entry from the polymer (do this for
h1 using atom type and resnum range, and then again for ca and a resnum
range).
Then you can change the matrix for the pair involving specific
combinations, but since thr have the same type name you'd need to include
the resnum again. Check the results carefully using printdetails and
printljmatrix.
On Fri, Aug 16, 2024, 5:10 AM Prof. Mark Wilson via AMBER <amber.ambermd.org>
wrote:
> hI,
>
> I am wanting to setup a hamiltonian replica exchange simulation
> where, in successive replicas, the interaction between a polymer and a
> surface
> are reduced (by reducing the vdw interactions).
>
> I naively thought I would be able to use parmed to do this.
> So, for example, I would use lines such as
> changeLJPair :98-1297.%h1 :1-97.%ca 1.3870 0.00157
>
> but I think what this does is change all the h1-ca interactions in the
> system
> not the ones between the surface (residues 98-1297) and polymer
> (residues 1-97);
> and in addition alters 1-4 interactions
>
> my question is essentially, is there another way to do this
> so that I can have simulations in which the interaction is weakened
> (this is to improve exploration of the surface by the polymer)
>
> Mark
>
> --
> Prof. Mark R. Wilson
> Department of Chemistry
> University of Durham
> South Road
> Durham
> DH1 3LE
> =========================
> Tel: +44 (0) 191 334 2144
> Fax: +44 (0) 191 384 4737
> =====================================================
> https://www.dur.ac.uk/chemistry/staff/profile/?id=206
> =====================================================
> http://www.dur.ac.uk/mark.wilson
> ====================================
> http://orcid.org/0000-0001-6413-2780
> ====================================
> “If you want advice for what you should do,
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Received on Fri Aug 16 2024 - 05:00:02 PDT
