Hi Justin, That's the .mdp file. dt = 0.0001 tinit = 0 nsteps = 100000 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.2 coulombtype = reaction-field-zero epsilon_rf = 0 rcoulomb = 0.1 rvdw = 0.2 vdwtype = cutoff pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 ref_t = 300 300 tc_grps = CNT water
unwanted temperatures from the 2nd computer are: 0.000000 569.41912 487.04663 428.94406 548.68127 406.10748 533.70324 487.37088 456.60519 452.93588 442.06088 463.36178 472.95275 502.68411 421.56173 492.36709 537.82879 483.68277 475.07675 494.39749 452.90744 494.20474 474.09298 482.93124 487.88989 509.66070 454.61138 453.75927 460.47540 454.69632 505.48443 485.54705 472.73492 460.27398 493.66903 480.78952 482.55233 470.91381 496.23098 484.82730 455.13006 469.39798 506.39819 479.32211 500.88891 485.77325 489.26815 476.03207 469.77734 466.56793 493.62396 482.78839 470.33157 462.17074 477.09906 470.76757 489.31381 486.11468 475.64276 471.49072 482.00595 485.38873 480.53643 475.79977 469.22253 488.72970 481.01446 493.13934 486.96911 481.62371 469.96023 488.82580 482.96316 476.70632 487.02590 487.53659 476.29904 472.44818 479.97314 477.46865 473.29275 469.93447 474.75863 472.98861 478.05273 486.17233 480.43383 475.78836 482.39563 480.41461 476.73916 490.22122 482.99255 478.54370 480.67889 478.16925 479.58938 474.47232 484.70156 484.90008 481.15057 --------------------------------- wanted temperatures from the 1st computer: 0.000000 326.691895 294.764709 298.554596 282.649414 307.463135 291.600189 300.543671 299.999359 297.054443 305.510986 303.078583 299.970428 299.137207 297.810272 298.365875 298.783813 301.805695 303.370575 300.340332 301.656372 299.389984 300.836243 296.977936 298.827637 299.861847 300.578522 296.483398 296.462646 302.666473 297.978180 304.715515 300.773193 300.172913 307.178711 298.444183 312.749542 302.172089 301.957428 303.820526 303.579712 296.149872 296.983826 303.023834 299.992371 299.144897 295.766663 305.296722 304.449219 309.249756 302.303375 304.800293 301.949646 302.895538 307.148254 298.277069 302.761719 296.531281 296.709900 298.417542 300.391022 297.293732 299.136353 290.259125 299.269531 305.229675 301.938751 301.106384 301.689117 295.249969 298.655914 296.441071 300.491364 304.039795 301.149384 295.906250 300.652557 296.303467 300.960083 304.725067 291.927765 303.753845 300.202393 294.915588 297.580017 302.882233 300.872406 306.164551 299.459473 300.940948 306.348328 299.031982 299.465942 297.603119 301.168304 305.233917 292.175751 304.453491 300.391571 303.061188 302.262146 Hope they are the data you wanted. Thanks for your time and help. On Tue, Mar 3, 2015 at 10:30 PM, mah maz <mahma...@gmail.com> wrote: > 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.