[gmx-users] RE: Gromos parameters for atom type OA
Samuli Ollila
Samuli.Ollila at fkem1.lu.se
Tue Dec 13 15:59:35 CET 2011
Hi all,
Thanks for the replies!
I was originally confused due to this sentence:
"The combination of the present carbohydrate parameter set with the 53A6 force field involves a
single change (slightly modified carbohydrate–oxygen to water–oxygen van der Waals repulsive inter
action parameter), but remains to be tested."
written in
Lins, R.D. & Hünenberger, P.H.
A new GROMOS force field for hexopyranose-based carbohydrates.
J. Comput. Chem., 26, 1400-1412 (2005).
However, interaction between carbohydrate–oxygen and water–oxygen seems to be the same in 45a3 and 53a6. Instead interactions between CH1, CH2, CH3 and carbohydrate–oxygen are different as Javier Cerezo already wrote before.
BR,
Samuli Ollila
>Date: Mon, 12 Dec 2011 10:47:23 +0100
>From: Patrick Fuchs <patrick.fuchs at univ-paris-diderot.fr>
>Subject: Re: [gmx-users] Gromos parameters for atom type OA
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4EE5CDAB.9080002 at univ-paris-diderot.fr>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>Hi,
>slightly off-thread, I'd like to add that the oxygen parameters of 53a6
>have been recently refined in a new set called 53a6OXY
>(http://pubs.acs.org/doi/abs/10.1021/ct1006407). So this ends up in new
>values for LJ and charges for the OA atom (as well as for other oxygen
>atoms).
>Cheers,
>Patrick
>Le 09/12/2011 20:03, Javier Cerezo a ?crit :
>> GROMOS force field builds the LJ parameters by multiplication of the
>> square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12)
>> labels). In the case of the repulsion term (C12), up to three of such
>> parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when
>> combined with other atoms, depending on the desired repulsion strength
>> (e.g. the enhanced C12(3) repulsion is used to keep charged groups
>> separated). Which of the three is used depends on the combination of
>> atoms, and is specified in an (asymmetric) matrix (see pages 14 and 15
>> in the pdf pages of 45a3 and 54a6 force fields from the GROMOS site, or
>> in the ifp file the last lines for each atom type containing "1", "2"
>> and "3"). For the case of OA, this matrix specifies that the second C12
>> term is to be used when OA encountes another OA. So, according, to the
>> ifp line you showed:
>>
>> C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 * 1.227E-3 =
>> 1.50553E-6
>>
>> Which is the same for 45a3 and 54a6 force fields.
>>
>> Differences in the parameters will show up only in the cases where the
>> SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2))
>>
>> Javier
>>
>>> El 09/12/11 16:12, Samuli Ollila escribi?:
>>> Dear all,
>>>
>>> I was comparing Gromos 45a3 and 53a6 force fields and I found
>>> something which I cannot understand. The atom type OA is described in
>>> ffG45a3nb.itp as:
>>> ;name at.num mass charge ptype c6 c12
>>> OA 8 0.000 0.000 A 0.0022619536 1.505529e-06
>>> and in ffG53a6nb.itp:
>>> OA 8 0.000 0.000 A 0.0022619536 1.505529e-06
>>> which are same parameters.
>>>
>>> However, according to Gromos developers the atom type OA has been
>>> changed between Gromos 45a3 and 53a6. The parameters given by Gromos
>>> developers for 45a3 are
>>> # IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3))
>>> 3 OA 0.04756 1.1250E-3 1.227E-3 0.0
>>> and for 53a6
>>> 3 OA 0.04756 1.100E-3 1.227E-3 0.0
>>>
>>> The actual numbers are different for parameters used in Gromacs since
>>> the way to write parameters is different.
>>>
>>> My problem is that there is difference in OA type between 45a3 and
>>> 53a6 in parameters given by Gromos developers but not in the files
>>> distributed in Gromacs package. Can someone explain this?
>>>
>>> BR,
>>> Samuli Ollila
>>>
>>>
>>
>> --
>> Javier CEREZO BASTIDA
>> Ph.D. Student
>> Physical Chemistry
>> Universidad de Murcia
>> 30100, Murcia (SPAIN)
>> T: (0034)868887434
>>
>
>
--
_______________________________________________________________________
Patrick FUCHS
Dynamique des Structures et Interactions des Macromol?cules Biologiques
INTS, INSERM UMR-S665, Universit? Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
E-mail address: patrick.fuchs at univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs
------------------------------
Message: 5
Date: Mon, 12 Dec 2011 10:42:31 +0100
From: Patrick Fuchs <patrick.fuchs at univ-paris-diderot.fr>
Subject: Re: [gmx-users] REST simulation
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4EE5CC87.4020905 at univ-paris-diderot.fr>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Otto,
in my lab we tried to implement this REST variant in GROMACS as proposed
by those authors. We figured out that it was easier to manipulate
directly the parameters files in the top directory. There you know
exactly what you are doing; recall that some interactions (i.e.
solvent/solvent) mustn't be scaled whereas some others have to be scaled
(solute/solute and solute/solvent).
It's probably possible to do it in the tpr file, but it looked less
trivial to me: i) you have to know how atoms are coded in the file (e.g.
in the functype[???]=LJ_SR[...] matrix, you have to understand how atom
numbers are coded there), ii) you have to regenerate a tpr from plain
text file; it's probably doable, but I don't know how. Actually, maybe
some developers can tell if it's possible.
Good luck,
Patrick
Le 08/12/2011 19:01, Otto Master a ?crit :
> Dear gromacs users,
>
> Recently I stumbled over following paper:
> T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a
> Variant of the Replica Exchange with Solute Tempering in GROMACS.
> Journal of Computational Chemistry 32 (2011) 1228-1234.
>
> The authors suggested an easy way to run this kind of simulation with
> Gromacs, without even changing the code. The only thing that is need, is
> the the rescaling of the parameters in the parameter file. Since the
> reduction of the replica number is quite appealing to me I wonder which
> file I have to change? Actually, I thought of manipulating the .tpr file
> or to rescale and creating the force fields for every replicate. Is this
> feasible, or is there a better way?
>
> Manipulating the .tpr file could be easier, since it unifies (right?)
> the parameters from the different force fields, before sending it to the
> mdrun application. But for this I would like to understand the tpr file
> first.There are quite a lot of entries and first I try to understand LJ
> interactions and how they are defined in this file. I found two entries
>
> LJ14
> functype[154]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00,
> c6B= 0.00000000e+00, c12B= 0.00000000e+00
> functype[155]=LJ14, c6A= 4.46680887e-03, c12A= 4.74702711e-06,
> c6B= 4.46680887e-03, c12B= 4.74702711e-06
>
> which corresponds to following interactions
>
> LJ-14:
> nr: 876
> iatoms:
> 0 type=154 (LJ14) 0 4
> 1 type=155 (LJ14) 0 5
>
> When I tried to calculate the parameters from the combination rules (in
> this case Gromos 53A6 force field), I found (the highlighted columns
> contain the original parameters for the specific atom groups from the
> Gromos documentation and the calculated value for combining the two
> parameters:
>
>
>
>
> sqrt(C6i) (from ff) sqrt(C6j) (from ff) sqrt(C6i)*sqrt(C6j) value
> from tpr file
> functype[154]=LJ14, c6A= CH3 H 0.09805 0 0 0.00E+00
> functype[155]=LJ14, c6A= CH3 CH1 0.09805 0.0779 0.007638095 4.47E-03
> functype[156]=LJ14, c6A= C CH2 0.04838 0.08642 0.004181 3.33E-03
> functype[157]=LJ14, c6A= C C 0.04838 0.04838 0.002340624 2.34E-03
>
>
> The values for N, C, O, H seems to be OK, but I have problems to get the
> same value, when CH1, CH2, CH3 are involved. Since I do not have too
> much experience, I would like to know how the value from the .tpr file
> can be derived.
>
> The other entry for LJ potential is the short range term LJ_SR (.tpr file
>
> ffparams:
> atnr=11
> ntypes=170
> functype[0]=LJ_SR, c6= 9.61380266e-03, c12= 2.66462448e-05
> functype[1]=LJ_SR, c6= 4.74365894e-03, c12= 1.14699596e-05
> functype[2]=LJ_SR, c6= 4.66325786e-03, c12= 5.16199998e-06
>
> Unfortunately, I do not find the section where the function is assigned
> to a specific pair of interaction. Where are these functions assigned to
> a specific interaction? Furthermore, is it possible to distinguish
> between intra-nonbonded (solute-solute) and inter-bonded (water-solute)
> interaction?
>
> For you this might be an easy question to answer, and you immediately
> realize there is a beginner at work, but nevertheless I would appreciate
> any help.
>
> All the best
> Otto
>
>
--
_______________________________________________________________________
Patrick FUCHS
Dynamique des Structures et Interactions des Macromol?cules Biologiques
INTS, INSERM UMR-S665, Universit? Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19
E-mail address: patrick.fuchs at univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs
------------------------------
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