[gmx-users] question about preferred values in itp files
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Apr 14 06:22:44 CEST 2016
Hey,
In addition, for Q3, sure you can have a program build you acetonitrile
from the interactions. But what about cholesterol? Morphine? A protein? For
just a bit more complicated stuff, let alone the really complicated stuff,
you need to have coordinates to start with.
Cheers,
Tsjerk
On Apr 14, 2016 02:20, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
> On 4/13/16 1:53 PM, abhishek khetan wrote:
>
>> Dear gmx-users,
>>
>> I have the opls-aa forcefield file for acetonitrile. It looks something
>> like:
>>
>> -----------------------------------------------------------------------------------------------------------
>> [ moleculetype ]
>> ; Name nrexcl
>> ACN 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass
>> 1 opls_755 1 ACN C1 1 -0.08 12.01100
>> 2 opls_759 2 ACN H2 1 0.06 1.00800
>> 3 opls_759 3 ACN H3 1 0.06 1.00800
>> 4 opls_759 4 ACN H4 1 0.06 1.00800
>> 5 opls_754 5 ACN C5 2 0.46 12.01100
>> 6 opls_753 6 ACN N6 3 -0.56 14.00670
>>
>> -----------------------------------------------------------------------------------------------------------
>>
>> My topol.top file looks like
>>
>> -----------------------------------------------------------------------------------------------------------
>> #include "./oplsaa.ff/forcefield.itp"
>> #include "./oplsaa.ff/acn.itp"
>>
>> [ system ]
>> ; Name
>> ACN216
>>
>> [ molecules ]
>> ; Compound #mols
>> ACN 216
>>
>> -----------------------------------------------------------------------------------------------------------
>>
>> And the forcefield.itp looks like
>>
>> -----------------------------------------------------------------------------------------------------------
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 3 yes 0.5 0.5
>>
>> #include "ffnonbonded.itp"
>> #include "ffbonded.itp"
>>
>> -----------------------------------------------------------------------------------------------------------
>>
>> Needless to mention, that the ffbonded.itp and ffnonbonded.itp are the
>> standard files from the oplsaa.ff directory in which the opls_XYZ
>> [atomtypes]/[bondtypes]/[dihedraltypes] etc are defined.
>>
>> My questions now are these:
>>
>> 1. When the charge and mass are already mentioned in the ffbonded.itp and
>> ffnonbonded.itp files for each of the opls_XYZ entries, then why do we
>> specify it again in the acn.itp file? Which values are read in the
>> simulations? the one from ffnonbonded.itp or the ones from acn.itp ? In
>> acse the acn.itp values are preferred, does it mean that the epsilon and
>> sigma value are still read from the ffnonbonded.itp file ?
>>
>>
> Charges in ffnonbonded.itp are never used for anything. Values specified
> in a topology always override those in ff(non)bonded.itp; this hierarchy is
> explained in the manual.
>
> 2. BIGGER QUESTION: When i look at the ffnonbonded and ffbonded files - the
>> bondtypes are specified in terms of the atom symbols from atomtpes,
>> instead
>> of the . The ffnonbonded and non bonded have entries like:
>>
>> ------------------------------------------------------------------------------------------------------------
>> [ atomtypes ]
>> opls_001 C 6 12.01100 0.500 A 3.75000e-01
>> 4.39320e-01 ; SIG
>> opls_017 C 6 12.01100 0.700 A 3.75000e-01
>> 4.39320e-01 ; SIG
>> opls_026 C 6 12.01100 0.265 A 3.75000e-01
>> 4.60240e-01 ; SIG
>> ..........
>> [ bondtypes ]
>> C C3 1 0.15220 265265.6 ; END
>> C CA 1 0.14900 334720.0 ; wlj 8/97
>> C CB 1 0.14190 374049.6 ; GUA
>> C CM 1 0.14440 343088.0 ; THY
>> C CS 1 0.14900 334720.0 ;
>> ..........
>>
>> ------------------------------------------------------------------------------------------------------------
>>
>> As you see all the bondtypes involve C as one of the atom types - how does
>> gromacs know which atomtype to choose ?? there are multiple atomtypes
>> corresponding to the same symbol. Or are have the symbols been chosen in
>> such a way that when wither if opls 001/017/026 bonds with C3 then the
>> bond
>> distance
>>
>>
> The bonded parameter space is significantly smaller than the nonbonded
> parameter space. The translations are in ffnonbonded.itp so grompp knows
> how to map bonded and nonbonded types.
>
> 3. EVEN BIGGER QUESTION: From what I understand, once I specify the
>> opls_XYZ type for a certain atom in a given molecule along with
>> [bonds]/[dihedrals]/etc in the acn.itp, it reads all specifications along
>> with the equilibrium bond distances, the angles and all that stuff from
>> the
>> ffbonded.itp and ffnonbonded.itp files and constructs the equilibrium
>> geometry of the molecule by itself. Does that mean that any geometry
>> specified by me for a single molecule is henceforth irrelevant ? I have
>> geometry for acetonitrile, calculated at a very high level of quantum
>> chemistry, perhaps more accurate than the one supplied in the pdb file
>> that
>> came with the forcefield. However, this accurate geometry may not be
>> exactly the same as that constructed by gromacs from the ffbonded.itp and
>> ffnonbonded.itp. Why do then, people always provide a *pdb or *gro file
>> for
>> the molecule along with the itp. if one has the acn.itp and the
>> ffbonded.itp and ffnonbonded.itp files, the geometry can already be
>> constructed... or ?
>>
>>
> Nothing in GROMACS constructs coordinates like this. Your input geometry
> is read. The energies and forces are calculated using the equilibrium
> parameters in the force field and your input coordinates.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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