Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Man Hoang Viet]

> Date: Thu, 10 Dec 2015 18:02:32 -0700
> From: Michael Shirts <mrshi...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for
>   GROMACS
> Message-ID:
>   <CA+zJb=idFn0-7ZdQDKcK+0QH8HwyJPBsW=xt-=wsd7nqi-y...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Great!  It's important to have all data validated carefully. Have you
> put together a set of tests, with coverage of all the atom types and
> interaction types, showing that the molecules give the same energies
> in both GROMACS and AMBER?  Validating conversions is quite important
> so that people can trust the results.

I have considered every atoms, atom types, nonbonds and bonds interaction,
atoms in every residues and nucleic acids to make sure they are the same
as in AMBER. If some ones pick up any those things to compare with
original one, I can make sure they will be the same. As you said the test
is very important, but it takes a lot of time and I am working on this. It
will be much better if other gromacs users like you participate the
testing work.

>
> On Thu, Dec 10, 2015 at 4:01 PM, Man Hoang Viet <mhv...@ifpan.edu.pl>
> wrote:
>> Dear GROMACS Admins,
>>
>> I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
>> want to share them with all gromacs users. I have tried to upload it via
>> below link
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>> However, I can not do register to upload. Could you please tell me how I
>> can share the amber force fields to gromacs users.
>>
>> Thank you very much.
>>
>> Yours sincerely,
>> --
>> Viet Man,
>>
>> Postdoctoral Research Associate,
>> Physics Department, NCSU
>

Viet Man,
Postdoctoral Research Associate,
Physics Department, NCSU

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Justin Lemkul]

On 12/10/15 6:01 PM, Man Hoang Viet wrote:

Dear GROMACS Admins,

I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
want to share them with all gromacs users. I have tried to upload it via
below link
http://www.gromacs.org/Downloads/User_contributions/Force_fields
However, I can not do register to upload. Could you please tell me how I
can share the amber force fields to gromacs users.



Email Rossen to be registered as a contributor.  The instructions (and his 
email) are linked directly on the homepage.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Michael Shirts]

Great!  It's important to have all data validated carefully. Have you
put together a set of tests, with coverage of all the atom types and
interaction types, showing that the molecules give the same energies
in both GROMACS and AMBER?  Validating conversions is quite important
so that people can trust the results.

On Thu, Dec 10, 2015 at 4:01 PM, Man Hoang Viet  wrote:
> Dear GROMACS Admins,
>
> I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
> want to share them with all gromacs users. I have tried to upload it via
> below link
> http://www.gromacs.org/Downloads/User_contributions/Force_fields
> However, I can not do register to upload. Could you please tell me how I
> can share the amber force fields to gromacs users.
>
> Thank you very much.
>
> Yours sincerely,
> --
> Viet Man,
>
> Postdoctoral Research Associate,
> Physics Department, NCSU
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Man Hoang Viet]

Dear GROMACS Admins,

I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
want to share them with all gromacs users. I have tried to upload it via
below link
http://www.gromacs.org/Downloads/User_contributions/Force_fields
However, I can not do register to upload. Could you please tell me how I
can share the amber force fields to gromacs users.

Thank you very much.

Yours sincerely,
-- 
Viet Man,

Postdoctoral Research Associate,
Physics Department, NCSU


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.