Thank you very much. Really very helpful comments. -Swarnendu
On Thu, Mar 24, 2011 at 1:52 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 24/03/2011 4:38 PM, Swarnendu Tripathi wrote: > > Hi all, > > Thank you for the reply. The answer I got for the second question about > table-extension, I understand and agree with that. > > Regarding my first question I asked, I did not get any error with grompp > even when I tried rlist=rvdw=2.0 and rcoulomb=0. For this I used the no > cut-off conditions which I have mentioned below in my previous e-mail. I am > using Gromacs-4.0.7. Any further suggestions or comments will be very > helpful. > > > VDW interactions normally become insignificant much faster than Coulomb > interactions, so treating all Coulomb interactions and only some VDW > interactions is logical. However, performing the search for neighbours takes > time, and given that you are computing the distances already for their > Coulomb interaction, it is probably cheaper just to compute all the VDW > interactions, i.e. rlist=rvdw=0. This might be different if you had a lot of > atoms that had zero partial charge. > > Mark > > > On Thu, Mar 24, 2011 at 12:17 AM, Mark Abraham > <mark.abra...@anu.edu.au>wrote: > >> On 24/03/2011 1:34 PM, Itamar Kass wrote: >> >>> Hi Swarnendu, >>> >>> grompp will return errer unless rlist=rcoulomb=rvdw=0, so you should >>> stick to it. >>> >>> Cheers, >>> Itamar >>> >>> On 24/03/11 1:13 PM, Swarnendu Tripathi wrote: >>> >>>> Hello everybody, >>>> >>>> I want to use the no cut-off option in gromacs for the electrostatic >>>> interactions. In manual it says for this I need to define: pbc=no; >>>> nstlist=0; ns-type=simple and rlist=rcoulomb=rvdw=0 in the .mdp file. >>>> >>>> My questions are: >>>> >>>> 1. If I choose rcoulomb=0 and rlist=rvdw=2.0 is that a problem? Do you >>>> always recommend to use rlist=rcoulomb=rvdw=0 for no cut-off option? >>>> >>>> 2. How should I choose the table-extension parameter now? Before, with >>>> pbc=xyz (with cut-off) I used table-extension=rvdw+1/2*length of the >>>> longest >>>> diagonal of the box (approximately). I am also using a tabulated potential. >>>> >>> >> Since there is effectively no box once pbc=no, your tables need only be >> as long as the longest possible interaction, plus some margin for when the >> structure rearranges. >> >> Mark >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
