Manik Mayur wrote:
On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Manik Mayur wrote:
Hi,
Even though after going through the manual, I still have some
basic confusions regarding generating topologies.
1) I have generated an itp file after adding some Cl- ions using
genion. It goes like this:
This is unnecessary. Just #include "ions.itp" and the parameters
for Cl- for whatever force field you're using are included.
Thanks for the reply. I will try to follow your suggestion, but just for
clarification, setting nrexcl=0 will allow nb interaction between all
the atoms in a molecule?
Using nrexcl only applies to intramolecular nonbonded interactions. There has
to be some reason with nrexcl = 1 is specified for ions in ions.itp, but that
may have to do with something in the code. I suppose, in general, nrexcl = 0
would include all interactions, but you probably don't want to do that for most
molecules, since, i.e. neighboring (bonded) atoms interact principally through
the bonded interaction; nonbonded calculations should not be applied to this
atom pair.
[ moleculetype ]
; Name nrexcl
Cl_ion 0
[ atoms ]
; nr type resnr residue atom cgnr charge
mass typeB chargeB massB
1 CL- 1 Cl- Cl 1 -1
35.453 ; qtot -1
2 CL- 2 Cl- Cl 2 -1
35.453 ; qtot -2
3 CL- 3 Cl- Cl 3 -1
35.453 ; qtot -3
........
........
To allow nb interactions between all the atoms in the molecule
Cl_ion, is setting nrexcl = 0 okay?
2) In spce.itp provided with GROMACS,
[ moleculetype ]
; molname nrexcl
SOL 2
while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname nrexcl
SOL 1
why is the inconsistency?
Probably just a typo.
So the correct version will be nrexcl=2, which means atoms no more than
2 bonds away will be excluded from nb interactions. Is my undestanding
correct?
Should be.
-Justin
3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
recommended). Since SPC/E is one of the most used model, should
I consider using OPLS rather than GROMOS96, otherwise how
significant will be the errors?
An excellent comparison of different force fields and different
water models can be found in:
Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.
4) I am using GROMOS96 43a1, so am I allowed to change
combination rule to '2' ( '1' is the default). How
significantly will it affect the simulations?
I would say it invalidates everything. The defaults for combination
rules, bonded parameters, etc. are as much a part of each force
field as the atom types and charges.
-Justin
Any relevant idea/suggestion/reference is appreciated.
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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