thank you very much for the help,
I think that looks to work as intended!
Mark
On 16/08/2024 12:45, Carlos Simmerling wrote:
>
>
> You don't often get email from carlos.simmerling.stonybrook.edu. Learn
> why this is important <https://aka.ms/LearnAboutSenderIdentification>
>
>
> *[EXTERNAL EMAIL]*
> 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
> <http://orcid.org/0000-0001-6413-2780>
> ====================================
> “If you want advice for what you should do,
> invite scientists, ask scientists for their expertise....
> We want the science to be heard.” Greta Thunberg
>
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--
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,
invite scientists, ask scientists for their expertise....
We want the science to be heard.” Greta Thunberg
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Received on Fri Aug 16 2024 - 07:00:02 PDT
