[gmx-users] gromacs.org_gmx-users Digest, Vol 191, Issue 10

[Justin Lemkul]

On 3/7/20 2:10 PM, Eduardo Mayo wrote:
>>
>>
>> Hi!,
>>
> I mean the page
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
> has
> a amber14sb.ff.tar.gz amber14sb_OL15.ff_corrected-Na-cation-params.tar.gz
> but at the top of the page it is a warning that say "These force fields are
> provided by volunteer contributors on an as-is basis. The GROMACS team
> implies no warranty by hosting them here. If you plan to use any of these
> force fields, you should make sure you test them for correctness on your
> system. Please let people know what you observe (good or bad!)."
> So I was wondering if this force field is realable, like is the any
> publication which validate it's results?? Can I use them for my simulation?
> Everyone who report Amberff14SB using gromacs use this forcefield file??

You should ask the corresponding authors how the implemented the force 
field.

As with any user contribution, unless explicit validation has been done 
(e.g. comparing forces and energies of identical configurations in AMBER 
vs. GROMACS), you should be wary about using the force field files. Or 
do the validation yourself before basing your whole project on the 
contributed files. Some of the parameter sets have been validated, but 
most haven't.

-Justin

>
>> ---------- Forwarded message ----------
>> From: Alessandra Villa <alessandra.villa.biosim at gmail.com>
>> To: gmx-users at gromacs.org, "gromacs.org_gmx-users" <
>> gromacs.org_gmx-users at maillist.sys.kth.se>
>> Cc:
>> Bcc:
>> Date: Thu, 5 Mar 2020 10:23:42 +0100
>> Subject: Re: [gmx-users] Amber14SB
>> Hi,
>>
>> Here a page of force field in GROMACS
>> http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm
>> maybe it helps. I did not fully understand your question
>>
>> Best regards
>> Alessandra
>>
>> On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo <eduardomayoyanes at gmail.com>
>> wrote:
>>
>>> Hi!!
>>> I'm sorry if is the amber14sb poster on the gromacs download site good??
>>> I've seen the warning on the page and I don't know what to think.
>>> Thanks in advance.

-- 
==================================================

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================