That is a very valid point, Mark! and very well said indeed. Yes, you are absolutely correct that we were in a rush to get to the "equilibrium" point but it had to be pushed gently.
Thanks, Sapna On Mon, Aug 20, 2012 at 7:29 PM, Mark Abraham <[email protected]> wrote: > On 21/08/2012 9:02 AM, Sapna Sarupria wrote: >> >> Thanks Mark. >> >> I also discovered that if I set the value of nstpcoule = 1 explicitly >> in my mdp file, it runs with the newer version of Gromacs 4.5.5 which >> was not the case earlier. > > > Yes, default behaviour of this kind of thing has varied over time. Again, > small changes in inputs can have big changes in output. To insulate yourself > from such things, equilibrate gently. > > >> Can you tell me what this variable does exactly? > > > Manual 7.3.15 :-) > > >> Will your suggestion >> that the initial setup might be faulty still be valid? > > > I didn't say the starting configuration was faulty - just that you were > likely being too rough with it. The children's swings at the park are > designed to be pushed along an equilibrium plane, but if you start the swing > off that plane and maybe push in a strange direction, don't be surprised if > the child cries :-) > > Mark > > >> >> Thanks, >> Sapna >> >> On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham <[email protected]> >> wrote: >>> >>> On 21/08/2012 8:45 AM, Sapna Sarupria wrote: >>>> >>>> Hello All, >>>> >>>> I have been having rather bizarre experience with Gromacs and was >>>> wondering if any one can shed some light on what is happening. I am >>>> running simulations of a hydrate + water system (think of hydrate as >>>> ice if you are not familiar with them). So basically I have a simple >>>> solid+liquid system. The system is minimized. The water model I am >>>> using is TIP4P/2005. Now when I run the simulation using grompp and >>>> mdrun both from Gromacs 4.5.5, my system crashes and writes out >>>> step*.pdb files. This I know happens when the system is exploding or >>>> something however, I do not see an obvious reason for this. >>>> However, if I compile the tpr file with older Gromacs version 4.0.5 >>>> and then use mdrun from 4.5.5 to run the simulation, my simulation >>>> proceeds just fine....the way I expect it to. >>> >>> >>> Minor differences in how things are constructed can have big effects on >>> numerical integration. MD is chaotic. >>> >>> >>>> Can anyone tell me what might be happening here. I have pasted my mdp >>>> file below. I think this might be related to the constraint algorithm >>>> but I have no idea how to fix it. I have tried using Lincs instead of >>>> Shake and that also gives the same outcome. Runs with Gromacs 4.0.5 >>>> (i.e. grompp using 4.0.5 and mdrun using 4.5.5) and fails with 4.5.5 >>>> (both grompp and mdrun using 4.5.5). >>>> >>>> Please let me know if you need any further information and thanks a >>>> lot for your help. Any insight will be helpful. >>>> >>>> #### BEGIN MDP FILE ####### >>>> title = s1-Hydrate melting simulation >>>> dt = 0.002 ; time step >>>> nsteps = 5000 ; number of steps >>>> nstcomm = 10 ; reset c.o.m. motion >>>> nstxout = 7500 ; write coords >>>> nstvout = 7500 ; write velocities >>>> nstlog = 25000 ; print to logfile >>>> nstenergy = 250 ; print energies >>>> xtc_grps = System >>>> nstxtcout = 25 >>>> nstlist = 10 ; update pairlist >>>> ns_type = grid ; pairlist method >>>> coulombtype = PME >>>> rvdw = 1.20 ; cut-off for vdw >>>> rcoulomb = 1.20 ; cut-off for coulomb >>>> rlist = 1.20 ; cut-off for coulomb >>>> Tcoupl = Nose-Hoover >>>> ref_t = 200.0 >>>> tc-grps = System >>>> tau_t = 0.5 >>>> Pcoupl = Parrinello-Rahman >>>> Pcoupltype = semiisotropic ; pressure geometry >>>> tau_p = 1.0 1.0 ; p-coupoling time >>>> compressibility = 4.5e-5 4.5e-5 ; compressibility >>>> ref_p = 100.0 100.0 ; ref pressure >>>> DispCorr = EnerPres ; long range correction >>>> gen_vel = yes ; generate init. vel >>>> gen_temp = 200 ; init. temp. >>>> gen_seed = 98247 ; random seed >>>> constraints = hbonds ; constraining bonds with H >>>> constraint_algorithm = shake >>>> >>> As you will see in >>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up, the problem >>> is >>> usually not with the constraints, but they're the first thing to show >>> deviant behaviour. Your use of T and P coupling algorithms is likely >>> inappropriate for equilibration given your starting point. Equilibrating >>> initially with Berendsen and/or a small time step will likely move you to >>> a >>> point where you can switch to the algorithms that produce proper >>> ensembles. >>> >>> Mark >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Only plain text messages are allowed! >>> * 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 > * Only plain text messages are allowed! > * 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 -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
