Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the . gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks!
On Tue, Mar 3, 2015 at 10:41 AM, mah maz <mahma...@gmail.com> wrote: > 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.