[gmx-users] atom types
Gavin Melaugh
gmelaugh01 at qub.ac.uk
Tue Aug 2 13:07:07 CEST 2011
Hi Mark
Thanks for the reply.
I am currently reading that section of the manual and, unless I am
completely mistaken, it seems to vindicate what I am saying.
"Extra Lennard-Jones and electrostatic interactions between pairs of
atoms in a molecule can be added in the [pairs] section of a molecule
definition".
In my [atom types] directive I have atomtype, charge mass, sigma and
epsilon etc. All nonbonding parameters are then calculated according to
the combination rule (in my case 3). 1-4 interactions are then
calculated based on the information in [pairs] directive (all atoms are
three bond away). I just have the atom indices of each pair in this
directive therefore with gen_pairs = yes, the interaction parameters
between each pair (which are 1-4) are calculated based on Fudge LJ and
Fudge QQ (which are both 0.5 in my case). All of this in conjunction
with nrexcl =3. Or am I completely wrong?
In my set up then, are 1-4 Coulombic interactions determined by the pair
list and fudge QQ?
Many Thanks
Gavin
Mark Abraham wrote:
>
>
> On 02/08/11, *Gavin Melaugh * <gmelaugh01 at qub.ac.uk> wrote:
>> Hi Justin
>>
>> Again thanks for the reply. I am not disagreeing with you but If I don't
>> include a [pairs] directive in the topology file (with gen_pairs =yes),
>> then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log
>> file. When I include the [pair s] directive then both types of
>> interaction are written to the log file. Therefore does gen_pairs= yes +
>> [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ
>> and QQ?
>
> Does manual section 5.3.4 answer your question?
>
> Mark
>
>>
>> Thanks
>>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>> >
>> >
>> > Gavin Melaugh wrote:
>> >> Hi Justin
>> >>
>> >> Sorry to labour on this but:
>> >>
>> >> I don't quite understand what you mean when you say that nonbonded
>> pair
>> >> interactions are not Coulombic. Surely nonbonded charged atoms
>> interact
>> >> with each other, when close enough? (or by Nonbonded pair interactions
>> >> do you explcitly mean 1-4,1-5, etc.)
>> >> What are the 1-4 Coulombic interactions generated by, if not by
>> >> gen_pairs =yes in my case?
>> >> I have read this section of the manual loads and though I had a
>> >> comprehensive understanding of it, but now I am confused again.
>> >>
>> >
>> > Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the
>> > purpose of [pairtype] generation is for LJ terms only. They are
>> > special 1-4 interactions between different atomtypes. Look at any
>> > force field for which [pairtypes] are listed - they have only C6 and
>> > C12 terms. Charges are not used for these calculations, but they are
>> > applied later during the MD using normal Coulombic equations and
>> FudgeQQ.
>> >
>> > -Justin
>> >
>> >> Thanks
>> >>
>> >> Gavin
>> >> Justin A. Lemkul wrote:
>> >>>
>> >>> Gavin Melaugh wrote:
>> >>>> Hi Justin
>> >>>>
>> >>>> I have checked the tpr file. Now it seems to assign the the two
>> >>>> type of
>> >>>> CHs as the same atom type, but at the same time with the specified
>> >>>> charge from the [atoms] directive, as I expected. Concerning 1-4
>> >>>> interactions and gen_pairs =yes, my concern is this; from the pair
>> >>>> list
>> >>>> and using gen_pairs = yes, does grompp then take the 1-4 coulombic
>> >>>> interaction for CH from the [atomtypes] directive (as the meaning of
>> >>>> gen_pairs =yes)?
>> >>>> Or does it assign the charge based on the atom index in the pair
>> list?
>> >>>>
>> >>> Charges are irrelevant for generation of pair interactions.
>> Nonbonded
>> >>> pair interactions are LJ, not Coulombic. You will certainly have 1-4
>> >>> Coulombic interactions, but they are not generated by gen_pairs. See
>> >>> manual section 5.3.4.
>> >>>
>> >>> -Justin
>> >>>
>> >>>> Many Thanks
>> >>>>
>> >>>> Gavin
>> >>>>
>> >>>> Justin A. Lemkul wrote:
>> >>>>> Gavin Melaugh wrote:
>> >>>>>> Hi all
>> >>>>>>
>> >>>>>> A very quick question. I have an atom-type labelled CH in the
>> >>>>>> atom-types
>> >>>>>> with a particular charge, and in the atom list I assign some of
>> >>>>>> these
>> >>>>>> specific atoms with zero charge as below. When I generate 1,4
>> >>>>>> interactions using gen_pairs =yes, what charge for the CH type
>> >>>>>> does it
>> >>>>>> use? Does gromacs assign the CH with the different charge as a new
>> >>>>>> atom
>> >>>>>> type.
>> >>>>>>
>> >>>>> Charges set in [atomtypes] are not used. The zero charge is
>> >>>>> assigned. Verify this by using gmxdump on your .tpr file.
>> >>>>>
>> >>>>> -Justin
>> >>>>>
>> >>>>>> ;Parameter level
>> >>>>>> [defaults]
>> >>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> >>>>>> 1 3 yes 0.5 0.5
>> >>>>>>
>> >>>>>> [atomtypes]
>> >>>>>> ;type mass charge ptype sigma(nm)
>> >>>>>> epsilon(kjmol-1)
>> >>>>>> CB 12.011000 0.000000 A 0.355000
>> >>>>>> 0.292880
>> >>>>>> CA 12.011000 -0.115000 A 0.355000
>> >>>>>> 0.292880
>> >>>>>> HC 1.008000 0.115000 A 0.242000
>> >>>>>> 0.125520
>> >>>>>> CU 13.019000 0.265000 A 0.350000
>> >>>>>> 0.334720
>> >>>>>> NU 14.007000 -0.597000 A 0.325000
>> >>>>>> 0.711280
>> >>>>>> CH 13.019000 0.332000 A 0.385000
>> >>>>>> 0.334720
>> >>>>>> C3 15.035000 0.000000 A 0.391000
>> >>>>>> 0.669440
>> >>>>>> C2 14.027000 0.000000 A 0.390500
>> >>>>>> 0.493712
>> >>>>>>
>> >>>>>> ;Molecular level
>> >>>>>> [moleculetype]
>> >>>>>> ; name nrexcl
>> >>>>>> isotridecylcage 3
>> >>>>>>
>> >>>>>> [atoms]
>> >>>>>> .................
>> >>>>>> 72 CH 1 CGE CH 24 0.3320
>> 13.0190
>> >>>>>> 73 C2 1 CGE C2 25 0.0000
>> >>>>>> 14.0270
>> >>>>>> 74 C2 1 CGE C2 25 0.0000
>> >>>>>> 14.0270
>> >>>>>> 75 C2 1 CGE C2 25 0.0000
>> >>>>>> 14.0270
>> >>>>>> 76 C2 1 CGE C2 26 0.0000
>> >>>>>> 14.0270
>> >>>>>> 77 C2 1 CGE C2 26 0.0000
>> >>>>>> 14.0270
>> >>>>>> 78 C2 1 CGE C2 26 0.0000
>> >>>>>> 14.0270
>> >>>>>> 79 C2 1 CGE C2 27 0.0000
>> >>>>>> 14.0270
>> >>>>>> 80 C2 1 CGE C2 27 0.0000
>> >>>>>> 14.0270
>> >>>>>> 81 C2 1 CGE C2 27 0.0000
>> >>>>>> 14.0270
>> >>>>>> 82 C2 1 CGE C2 28 0.0000
>> >>>>>> 14.0270
>> >>>>>> 83 CH 1 CGE CH 28 0.0000
>> >>>>>> 13.0190
>> >>>>>> 84 C3 1 CGE C3 29 0.0000
>> >>>>>> 15.0350
>> >>>>>>
>> >>>>>>
>> >>>>>> Many Thanks
>> >>>>>>
>> >>>>>> Gavin
>> >>
>> >
>>
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