On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul <[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? [ 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? > 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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