Hi,<br><br>Even though after going through the manual, I still have some basic confusions regarding generating topologies.<br><br>1) I have generated an itp file after adding some Cl- ions using genion. It goes like this:<br>
<br>[ moleculetype ]<br>; Name nrexcl<br>Cl_ion 0<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 CL- 1 Cl- Cl 1 -1 35.453 ; qtot -1<br>
2 CL- 2 Cl- Cl 2 -1 35.453 ; qtot -2<br> 3 CL- 3 Cl- Cl 3 -1 35.453 ; qtot -3<br>........<br>........<br><br>To allow nb interactions between all the atoms in the molecule Cl_ion, is setting nrexcl = 0 okay?<br>
<br>2) In spce.itp provided with GROMACS, <br>
<br>
[ moleculetype ]<br>
; molname nrexcl<br>
SOL 2<br>
<br>
while in the manual, on pg. 100 (Chapter-5 Topologies)<br>
[ moleculetype ]<br>
; molname nrexcl<br>
SOL 1<br>
<br>
why is the inconsistency?<br>
<br>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? <br>
<br>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?<br><br>Any relevant idea/suggestion/reference is appreciated.<br>
<br>Thanks,<br><br clear="all">Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>