[gmx-users] How to install a new force-field?

[Justin Lemkul]

On 12/23/18 9:54 AM, ZHANG Cheng wrote:
> Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as shown on
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

Yes, because it was my idea to implement it :)

>
> I want to make sure the CHARMM36m is used instead of CHARMM36.

Then don't add any define statement in your .mdp file. C36m is the 
default parameter set. For people who want the old C36 (for testing, 
compatibility with old work, etc), specify "define = -DUSE_OLD_C36" in 
the .mdp file.

-Justin

>
>
>
>
>
> ------------------ Original ------------------
> From:  "ZHANG Cheng"<272699575 at qq.com>;
> Date:  Sun, Dec 23, 2018 10:38 PM
> To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
>
> Subject:  How to install a new force-field?
>
>
>
> Dear Gromacs users,
>
>
> In the pdb2gmx command, we are asked to select the force field to simulate our protein system. I am told that a99SB-disp and CHARMM36m are better force-field for the proteins. But both of them are not the default ones. Can I ask
>
>
> 1) What is the latest officical website to download them?
> At this website,
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
> I could not find a99SB-disp and CHARMM36m.
>
>
> 2) How to install them?
> Is there a step-by-step instruction for the installation?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
>
>
> CHARMM36m: an improved force field for folded and intrinsically disordered proteins
> https://www.nature.com/articles/nmeth.4067
>
>
> a99SB-disp:
> Developing a molecular dynamics force field for both folded and disordered protein states
> https://www.pnas.org/content/115/21/E4758

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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