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Re: [lammps-users] Amber FF
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Re: [lammps-users] Amber FF


From: Andrew Jewett <jewett@...1937...>
Date: Thu, 5 Oct 2017 18:57:59 -0700

On Wed, Oct 4, 2017 at 9:20 PM, Hossein Geraili <geraili.hsn@...24...> wrote:
thank you for your detailed answer. Actually, it is a little difficult for me to use moltemplate for my molecule( [BMIM][PF6] ionic liquid), since the examples of moltemplate for Amber are not really helpful for my molecule( with atm_style full). Could you please send me some example or tutorial about amber for a bigger molecule.
Best regards

   This is a legitimate point.  I made the AMBER force field available, but I do not use it for my own work.  So I do not have the time to make more examples and test them, aside from the few that are already there.

   I would love to solve this problem by crowdsourcing.  I would love to encourage people to submit their example molecules in moltemplate (or even LAMMPS) format.  If they do (either by email, or by github), I will include them with moltemplate.  If it would help to put a button on the moltemplate web page along with a web form, I am happy to do that.

   For now, if you do not mind switching force fields, then try the ATB database.  It contains molecule force field parameters and partial charges for a huge variety of organic molecules in moltemplate (.LT) format.  I think it is free (for academic use).  These molecules are presumably not compatible with the AMBER force field.

https://atb.uq.edu.au/

BMIM is currently here:
https://atb.uq.edu.au/molecule.py?molid=1699
(however they may change the URL in the future.  If so, enter "BMIM" into the search page)

Click on "Molecular Dynamics (MD) Files", and select "LAMMPS" from the "Format" pull-down menu.

Cheers
Andrew




 

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On Thu, Oct 5, 2017 at 1:31 AM, Andrew Jewett <jewett@...1937...> wrote:
Dear Hossein

   The moltemplate implementation of the GAFF forcefield has been tested by several people and they say it is accurate now.  (It wasn't at first.  The GAFF2 force field probably works as well because it was automatically converted from a file with an identical file format as GAFF.  But it has not yet been tested.)

   The main issues with using GAFF/GAFF2 in moltemplate are:
1) If my understanding is correct, it was not intended for proteins and nucleic acids.  It was intended for small organic molecules.  Hopefully that's not a problem for you.

2) Moltemplate does not calculate the partial charge on each atom correctly for the AMBER force fields.  Moltemplate is a (relatively) simple database lookup program.  It does not perform quantum-chemistry calculations to determine atomic charges (AmberTools does this).  You will have to use AmberTools or some other quantum code to calculate them (or lookup the partial charges from "oplsaa.lt".  That's what the AMBER examples which come with moltemplate do.) .  Afterwards, you can use commands like
set atom 70 charge -0.212
  to assign partial charges to each atom.
and

On Wed, Oct 4, 2017 at 6:38 AM, Hossein Geraili <geraili.hsn@...24...> wrote:
Dear Andrew,
Do you think that Using GAFF codes in moltemplate would work for Amber force field? I don't see the difference, but I am not sure about that.
Best regards



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On Wed, Oct 4, 2017 at 5:27 AM, Andrew Jewett <jewett@...1937...> wrote:
Good to know the existence of the GAFF2 force field.  I was unaware.  Added it to moltemplate today.  Thanks!

(...but I still didn't see any of Urey-Bradley terms that Hossein mentioned.)
-andrew

On Tue, Oct 3, 2017 at 6:13 PM, James Kress <jimkress_58@...5633...> wrote:

You’ll find gaff and gaff2 in amber16/dat/leap/parm

 

Jim

 

 

From: Andrew Jewett [mailto:jewett@...1937...]
Sent: Tuesday, October 03, 2017 8:05 PM
To: Hossein Geraili <geraili.hsn@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@...42...e.net>
Subject: Re: [lammps-users] Amber FF

 

 

 

On Tue, Oct 3, 2017 at 7:19 AM, Hossein Geraili <geraili.hsn@...24...> wrote:

E = K (theta - theta0)^2 + K_UB (r_13 - r_UB)^2
K_UB and r_UB(cross-term accounting for angle bending using 1,3 nonbonded interactions). How can I calculate these?

 

On Tue, Oct 3, 2017 at 5:33 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:

 

On Tue, Oct 3, 2017 at 9:37 AM, Hossein Geraili <geraili.hsn@...24...> wrote:

Dear Lammps users,

I am using Amber force field optimized for my molecule, and it(in the article) has only two parameters for the angle. In the lammps section Howto for Amber angle_style charmm in introduced, but for charmm angle_style one should specify 4 parameters( 2Urey_Bradley parameters). I simulated with harmonic and I get a big error. Any idea where should I find these Urey_Bradley parameters? Actually the "distance between the 1,3 atoms in the harmonic potential" which is the Rub(one of the parameters, I can find. But, what about the force constant?

 

here is the $5000 question: what is the force constant of term that does not exist?

 

axel.

 

 

    For what it's worth, there are no Urey-Bradley parameters listed in the "gaff.dat" file distributed with AmberTools.  (I have not looked at the other AMBER force-field files.)  Don't know if this helps.  Where are you reading about these Urey-Bradley parameters?

 

-andrew

 

 





--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7144....




--
Hosein Geraili Daronkola
M.Sc.Graduated of physical chemistry
Physical Chemistry,
Department of Chemistry,
Sharif University of Technology.
geraili_hosein@...7110...