[gmx-users] Hbond Shake and Gromacs Version Related
Sapna Sarupria
sapna.sarupria at gmail.com
Tue Aug 21 01:31:56 CEST 2012
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 <Mark.Abraham at anu.edu.au> 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 <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.
>>>
>>> Mark
>>> --
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>>
>>
>>
>
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--
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
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