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<div style="text-align: left;">Hi,<br><br>In 3.3 position restraints and NPT can also cause trouble when the amount of scaling is large.<br><br>In 4.0 there is the new refcoord_scaling option that allows scaling<br>of the position restraint reference coordinates or their COM.<br>We would also like to have such a scaling for frozen atoms,<br>but that is not implemented yet.<br><br>Berk<br></div></div></div><br><br><hr id="stopSpelling">> Date: Fri, 17 Oct 2008 07:57:34 -0400<br>> From: jalemkul@vt.edu<br>> To: viveksharma.iitb@gmail.com<br>> Subject: Re: [gmx-users] Error"Box was shifted at least 10 times. Please see log-file"<br>> CC: gmx-users@gromacs.org<br>> <br>> There are several potential problems all combined into one. As has been <br>> reported on the list, applying freezegrps, constraints, and pressure coupling <br>> all at the same time do not mix well. The best bet is to turn off the pressure <br>> coupling if you're set on using freezegrps. Otherwise, use position restraints <br>> if you require NPT.<br>> <br>> -Justin<br>> <br>> vivek sharma wrote:<br>> > Hi justin,<br>> > <br>> > thanks for your response.....<br>> > following is the .mdp file pasted..<br>> > <br>> > _____<br>> > title = trp_drg<br>> > warnings = 10<br>> > cpp = /lib/cpp ; location of cpp on SGI<br>> > define = -DPOSRES<br>> > constraints = all-bonds<br>> > integrator = md<br>> > dt = 0.002 ; ps !<br>> > nsteps = 2500000 ; total 5000.0 ps.<br>> > nstcomm = 1<br>> > nstxout = 25000 ; output coordinates every 0.5 ps<br>> > nstvout = 100000 ; output velocities every 2.0 ps<br>> > nstfout = 0<br>> > nstlog = 10<br>> > nstenergy = 10<br>> > nstlist = 10<br>> > ns_type = grid<br>> > rlist = 0.9<br>> > coulombtype = PME<br>> > rcoulomb = 0.9<br>> > rvdw = 1.0<br>> > energygrps_excl = freeze freeze freeze SOL ! To remove <br>> > computation of interactions between the frozen groups with surroundings (i.e. the solvent, SOL) <br>> > <br>> > fourierspacing = 0.12<br>> > fourier_nx = 0<br>> > fourier_ny = 0<br>> > fourier_nz = 0<br>> > pme_order = 6<br>> > ewald_rtol = 1e-5<br>> > optimize_fft = yes<br>> > ; Berendsen temperature coupling is on in four groups<br>> > Tcoupl = berendsen<br>> > tau_t = 0.1 0.1 0.1<br>> > tc_grps = protein sol NDP<br>> > ref_t = 300 300 300<br>> > ; Pressure coupling is on<br>> > Pcoupl = berendsen<br>> > pcoupltype = isotropic<br>> > tau_p = 0.5<br>> > compressibility = 4.5e-5<br>> > ref_p = 1.0<br>> > ; Generate velocites is on at 300 K.<br>> > gen_vel = yes<br>> > gen_temp = 300.0<br>> > gen_seed = 173529<br>> > ; Non-equilibrium MD stuff<br>> > freezegrps = freeze<br>> > freezedim = Y Y Y<br>> > ____<br>> > <br>> > With Thanks,<br>> > Vivek<br>> > <br>> > 2008/10/17 Justin A. Lemkul <jalemkul@vt.edu <mailto:jalemkul@vt.edu>><br>> > <br>> > <br>> > <br>> > vivek sharma wrote:<br>> > <br>> > Hi Tehre,<br>> > i am running a job by keeping a part of molecule freeze ....by<br>> > using the .mdp option....<br>> > <br>> > <br>> > What is your entire .mdp file?<br>> > <br>> > -Justin<br>> > <br>> > ______________<br>> > <br>> > ________<br>> > <br>> > energygrps_excl = Terminal Terminal Terminal SOL ! To<br>> > remove<br>> > computation of nonbonding interactions between the frozen groups<br>> > with each other<br>> > and surroundings (i.e. the solvent, SOL)<br>> > freezegrps = Terminal ! Index group to freeze<br>> > freezedim = Y Y Y ! Freeze this group in all<br>> > directions, x,<br>> > y, and z<br>> > ___________________________________________________<br>> > <br>> > <br>> > where frreze is a group mentioned in the index file...<br>> > During the run the job is being terminated with the following error<br>> > .<br>> > __________________________________________________________<br>> > Step 1 Warning: pressure scaling more than 1%, mu: -3.51079e+22<br>> > -3.51079e+22 -3.51079e+22<br>> > <br>> > -------------------------------------------------------<br>> > Program mdrun_d, VERSION 3.3.3<br>> > Source code file: ns.c, line: 258<br>> > <br>> > Fatal error:<br>> > Box was shifted at least 10 times. Please see log-file.<br>> > -------------------------------------------------------<br>> > <br>> > Error on node 0, will try to stop all the nodes<br>> > Halting parallel program mdrun_d on CPU 0 out of 24<br>> > <br>> > srun: error: n216: task0: Aborted<br>> > srun: Terminating job<br>> > __________________________________________________________________<br>> > <br>> > Can somebody give an insight in the problem for figuring out the<br>> > probable cause of the error.<br>> > <br>> > PS::Before the run I mentioned the boxsize in editconf as "-box<br>> > 7.5 5 6 ", to keep the size of box and number of solvent optimum.<br>> > Does it have anything to do with the mentioned error ?<br>> > <br>> > <br>> > Looking for suggestions..<br>> > with thanks,<br>> > Vivek<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > <mailto:gmx-users@gromacs.org><br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search<br>> > before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org<br>> > <mailto:gmx-users-request@gromacs.org>.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > -- <br>> > ========================================<br>> > <br>> > Justin A. Lemkul<br>> > Graduate Research Assistant<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > <br>> > ========================================<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > <mailto:gmx-users@gromacs.org><br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www<br>> > interface or send it to gmx-users-request@gromacs.org<br>> > <mailto:gmx-users-request@gromacs.org>.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? 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