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 <[email protected]>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 <[email protected]> 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 <[email protected]> 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 < > [email protected] > >>> > >>>> 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 < > >>>>> [email protected] > >>>>> > >>>>> 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 [email protected] > >>>>>> 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 [email protected]. > >>>>>> * 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 [email protected] > >>>>> 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 [email protected]. > >>>>> * 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 [email protected] > >>> 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 [email protected]. > >>> * 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 [email protected] > > 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 [email protected]. > > * 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
