On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur <[email protected]> wrote:
> Hi all, > > I have a few probIems/confusions and will be extremely thankful for any > help. I added some "Cl- ions" by replacing water using "genion (and -nn)". > It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I > try to run grompp, it gives an error saying "no such molecule type Cl". So > my questions are: > 1) How to avoid that error? Do I have to define a Cl.itp and add molecule > type etc. ? > 2) If I try to add Cl using -neutral option (as my system before already > had a net +ve charge), it says "No ions to add and no potentials to > calculate", why? > 3) Why is Cl listed in molecules and not [atoms] section? > 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using > ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else I > would have to do? > 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald > geom=3dc, other than using walls option(I have my own channel walls in the > system, so want to avoid them). Is there a way to use periodicity=xyz with > coulumb-type=PME and ewald geom=3dc? > Is there a way to use periodicity=xy with coulumb-type=PME and ewald geom=3dc? > > Thanks, > Manik > > -- > _________________ > HAPAX LEGOMENA > -- _________________ HAPAX LEGOMENA
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