Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you!
On Mon, Mar 2, 2015 at 10:08 PM, mah maz <mahma...@gmail.com> wrote: > Hi Justin, > So many thanks for your help. The problem was solved by changing cutoff to > reaction-field-zero and epsilon_rf=0. It just may need some modifications > for assigning right rvdw, rcoulomb and rlist. Thanks again! > Cheers > > > > On Mon, Mar 2, 2015 at 7:03 PM, mah maz <mahma...@gmail.com> wrote: > >> Dear Justin, >> Thank you very much for your answer. Cutoffs are not set by exact studies >> and as you said they are arbitrary. Actually I don't know how to choose >> them for my system. I have CNT in water not vacuo. I tried >> rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual >> but don't know how to set them. Have you got any ideas to help? >> thanks! >> Cheers >> >> On Sun, Mar 1, 2015 at 8:55 PM, mah maz <mahma...@gmail.com> wrote: >> >>> Dear Chaban, >>> >>> Thank you very much. Could you please explain more about the problem and >>> how I may fix it? >>> >>> Cheers >>> >>> On Sun, Mar 1, 2015 at 11:16 AM, mah maz <mahma...@gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> I have a CNT system. I have set the mdp file as follows, but the >>>> temperature output is logically more than what I expected even in the >>>> production step(around 500k). I have changed the mdp file several times but >>>> it doesn't work. What are the possible causes of problem? >>>> Thank you! >>>> dt = 0.0001 >>>> tinit = 0 >>>> nsteps = 2000000 >>>> nstxout = 1000 >>>> nstvout = 1000 >>>> nstfout = 0 >>>> nstlog = 1000 >>>> nstenergy = 1000 >>>> nstlist = 5 >>>> ns_type = grid >>>> rlist = 0.9 >>>> coulombtype = cut-off >>>> rcoulomb = 0.9 >>>> rvdw = 0.9 >>>> rvdw_switch = 0.5 >>>> vdwtype = switch >>>> pbc = no >>>> integrator = md-vv >>>> Tcoupl = nose-hoover >>>> tau_t = 0.1 >>>> ref_t = 300 >>>> tc_grps = CNT >>>> gen_temp = 300 >>>> pcoupl = no >>>> >>>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
