I reduced time step in equi.mdp file to 20 ps. But the system is still not balance. Should i continue reduce time step below 20 ps value ? Thanks so much for any suggestion about appropriate time step value !
Regards, KT On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen <kieuthu2...@gmail.com>wrote: > Thank Justin and Tsjerk so much for your help ! > I will try smaller time step. And i hope it work :-) > > Regards, > KT > > > On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > >> Well, 20-30 fs is fine with Martini. But you may have to take care >> initially, and start with a smaller time step. >> >> Cheers, >> >> Tsjerk >> >> On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> > >> > >> > On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote: >> > >> >> @Justin, >> >> Fmax=8.0226669e+00 >> >> >> > >> > OK, that looks good. >> > >> > >> > the system includes protein, lipid, water, ion Cl- >> >> >> >> em.mdp file is >> >> >> >> integrator = steep >> >> tinit = 0.0 >> >> dt = 0.02 >> >> nsteps = 50000 >> >> nstcomm = 1 >> >> nstxout = 5000 >> >> nstvout = 5000 >> >> nstfout = 0 >> >> nstlog = 1000 >> >> nstenergy = 1000 >> >> nstxtcout = 1000 >> >> xtc_precision = 1000 >> >> nstlist = 1 >> >> ns_type = grid >> >> pbc = xyz >> >> rlist = 1.4 >> >> coulombtype = Shift >> >> rcoulomb_switch = 0.0 >> >> rcoulomb = 1.2 >> >> epsilon_r = 15 >> >> vdw_type = Shift >> >> rvdw_switch = 0.9 >> >> rvdw = 1.2 >> >> DispCorr = No >> >> tcoupl = no >> >> pcoupl = no >> >> gen_vel = no >> >> constraints = none >> >> constraint_algorithm = Lincs >> >> continuation = no >> >> lincs_order = 4 >> >> lincs_warnangle = 30 >> >> >> >> >> >> equi.mdp file is >> >> >> >> integrator = md >> >> tinit = 0.0 >> >> dt = 0.03 >> >> >> > >> > Does a smaller time step work? I know the whole point of a MARTINI >> > simulation is to use a 20-40 fs time step, but in my (very very limited) >> > experience, nothing over 20 fs is consistently stable. Perhaps others >> with >> > better experience can offer pointers. >> > >> > -Justin >> > >> > >> > nsteps = 3000000 >> >> nstcomm = 1 >> >> comm-grps = >> >> nstxout = 5000 >> >> nstvout = 5000 >> >> nstfout = 0 >> >> nstlog = 1000 >> >> nstenergy = 1000 >> >> nstxtcout = 1000 >> >> xtc_precision = 100 >> >> xtc-grps = >> >> energygrps = >> >> nstlist = 10 >> >> ns_type = grid >> >> pbc = xyz >> >> rlist = 1.2 >> >> coulombtype = Shift >> >> rcoulomb_switch = 0.0 >> >> rcoulomb = 1.2 >> >> epsilon_r = 15 >> >> vdw_type = Shift >> >> rvdw_switch = 0.9 >> >> rvdw = 1.2 >> >> DispCorr = No >> >> tcoupl = Berendsen >> >> tc-grps = Protein DSPC Ion_W >> >> tau_t = 1.5 1.5 1.5 >> >> ref_t = 310 310 310 >> >> Pcoupl = Berendsen >> >> Pcoupltype = semiisotropic >> >> tau_p = 3.0 3.0 >> >> compressibility = 3e-4 3e-4 >> >> ref_p = 1.0 1.0 >> >> gen_vel = no >> >> constraints = none >> >> constraint_algorithm = Lincs >> >> continuation = no >> >> lincs_order = 4 >> >> lincs_warnangle = 30 >> >> >> >> Thanks so much for any help ! >> >> Regards, >> >> KT >> >> >> >> >> >> On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul <jalem...@vt.edu> >> wrote: >> >> >> >> >> >>> >> >>> On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote: >> >>> >> >>> Thank Tsjerk so much ! >> >>>> But after being minimized 50000 steps and equilibrated 90 ns, there >> are >> >>>> some bonds in the system that rotate more than 30 degrees. >> >>>> I applied tips for blew up system as you advised. But the system does >> >>>> not >> >>>> achieve balance. >> >>>> Should i carry out more many steps for minimization ? or minimize >> many >> >>>> times ? to get more equilibrated system. >> >>>> >> >>>> >> >>>> I would say that 50000 steps of minimization is far more than is >> >>> normally >> >>> necessary. What Fmax do you achieve at the end of EM? What is in the >> >>> system? What is in your .mdp file? Systems can randomly crash if the >> >>> model >> >>> physics breaks due to incorrect .mdp settings or an unstable topology. >> >>> >> >>> -Justin >> >>> >> >>> >> >>> On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar < >> tsje...@gmail.com >> >>> >> >>>> wrote: >> >>>>> >> >>>> >> >>>> Hi KT, >> >>>> >> >>>>> >> >>>>> This is caused by another problem. Your system blew up. Check >> messages >> >>>>> before this one, and check the log for LINCS warnings. >> >>>>> >> >>>>> Cheers, >> >>>>> >> >>>>> Tsjerk >> >>>>> >> >>>>> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen < >> >>>>> kieuthu2...@gmail.com >> >>>>> >> >>>>> wrote: >> >>>>>> >> >>>>>> >> >>>>> Dear All, >> >>>>> >> >>>>>> >> >>>>>> My MD simulation has an error >> >>>>>> >> >>>>>> Warning: Only triclinic boxes with the first vector parallel to the >> >>>>>> >> >>>>>> x-axis >> >>>>> >> >>>>> and the second vector in the xy-plane are supported. >> >>>>>> Box (3x3): >> >>>>>> Box[ 0]={ nan, nan, nan} >> >>>>>> Box[ 1]={ nan, nan, nan} >> >>>>>> Box[ 2]={ nan, nan, nan} >> >>>>>> Can not fix pbc. >> >>>>>> >> >>>>>> I searched on Gromacs-errors web, but i did not see this error. >> >>>>>> How can i fix it ? >> >>>>>> >> >>>>>> Thanks and regards, >> >>>>>> KT >> >>>>>> -- >> >>>>>> gmx-users mailing list gmx-users@gromacs.org >> >>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users< >> http://lists.gromacs.org/**mailman/listinfo/gmx-users> >> >>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>>>>> > >> >>>>>> * Please search the archive at >> >>>>>> http://www.gromacs.org/****Support/Mailing_Lists/Search< >> http://www.gromacs.org/**Support/Mailing_Lists/Search> >> >>>>>> <h**ttp://www.gromacs.org/Support/**Mailing_Lists/Search< >> 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< >> http://www.gromacs.org/**Support/Mailing_Lists> >> >>>>>> <http://**www.gromacs.org/Support/**Mailing_Lists< >> http://www.gromacs.org/Support/Mailing_Lists> >> >>>>>> > >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>> >> >>>>> -- >> >>>>> Tsjerk A. Wassenaar, Ph.D. >> >>>>> >> >>>>> post-doctoral researcher >> >>>>> Biocomputing Group >> >>>>> Department of Biological Sciences >> >>>>> 2500 University Drive NW >> >>>>> Calgary, AB T2N 1N4 >> >>>>> Canada >> >>>>> -- >> >>>>> gmx-users mailing list gmx-users@gromacs.org >> >>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users< >> http://lists.gromacs.org/**mailman/listinfo/gmx-users> >> >>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>>>> > >> >>>>> * Please search the archive at >> >>>>> http://www.gromacs.org/****Support/Mailing_Lists/Search< >> http://www.gromacs.org/**Support/Mailing_Lists/Search> >> >>>>> <h**ttp://www.gromacs.org/Support/**Mailing_Lists/Search< >> 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 >> <http://www.gromacs.org/**Support/Mailing_Lists> >> >>>>> <http://**www.gromacs.org/Support/**Mailing_Lists< >> http://www.gromacs.org/Support/Mailing_Lists> >> >>>>> > >> >>>>> >> >>>>> >> >>>>> -- >> >>> ==============================****========== >> >>> >> >>> Justin A. Lemkul, Ph.D. >> >>> Research Scientist >> >>> Department of Biochemistry >> >>> Virginia Tech >> >>> Blacksburg, VA >> >>> jalemkul[at]vt.edu | (540) 231-9080 >> >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin< >> http://vt.edu/Pages/Personal/justin> >> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin< >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >>> > >> >>> >> >>> ==============================****========== >> >>> >> >>> -- >> >>> gmx-users mailing list gmx-users@gromacs.org >> >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users< >> http://lists.gromacs.org/**mailman/listinfo/gmx-users> >> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>> > >> >>> * Please search the archive at http://www.gromacs.org/** >> >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >> >>> Mailing_Lists/Search< >> 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< >> http://www.gromacs.org/**Support/Mailing_Lists> >> >>> <http://**www.gromacs.org/Support/**Mailing_Lists< >> http://www.gromacs.org/Support/Mailing_Lists> >> >>> > >> >>> >> >>> >> > -- >> > ==============================**========== >> > >> > >> > Justin A. Lemkul, Ph.D. >> > Research Scientist >> > Department of Biochemistry >> > Virginia Tech >> > Blacksburg, VA >> > jalemkul[at]vt.edu | (540) 231-9080 >> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> > ==============================**========== >> > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/**mailman/listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > * Please search the archive at http://www.gromacs.org/** >> > Support/Mailing_Lists/Search< >> 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< >> http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Biocomputing Group >> Department of Biological Sciences >> 2500 University Drive NW >> Calgary, AB T2N 1N4 >> Canada >> -- >> 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