[gmx-users] Hbond Shake and Gromacs Version Related
Mark.Abraham at anu.edu.au
Tue Aug 21 01:29:17 CEST 2012
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 :-)
> On Mon, Aug 20, 2012 at 6:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au> 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.
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