<div dir="ltr">Hi,<div><br></div><div>This looks approximately normal for constrained dynamics of systems with water. See e.g. fig 8 of <a href="http://dx.doi.org/10.1016/j.cpc.2013.06.003">http://dx.doi.org/10.1016/j.cpc.2013.06.003</a><br><br>Mark</div><div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jul 15, 2015 at 5:57 PM Bernhard <<a href="mailto:b.reuter@uni-kassel.de">b.reuter@uni-kassel.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I now also tried with bigger manual rlist values of 1.02 and 1.05: This<br>
doesnt help - the drift of the conserved energy with Nose-Hoover gets<br>
even bigger: -1,8 kJ/mol/ps (7.9*10^-5 kJ/mol/ps per atom) and -2.62<br>
kJ/mol/ps (1.15*10^-4 kJ/mol/ps per atom).<br>
<br>
Am 15/07/15 um 17:41 schrieb Bernhard:<br>
> I mean a drift of the total energy in NVE - while with Nose-Hoover the<br>
> drift is in the Conserved-Energy quantity of g_energy (the total<br>
> energy shows no drift with Noose-Hoover...).<br>
><br>
> Am 15/07/15 um 17:38 schrieb Bernhard:<br>
>> I also did a NVE simulation with the same parameters, system and<br>
>> starting conditions but with manually set rlist=1.012nm (since<br>
>> verlet-buffer-drift doesnt work in NVE):<br>
>> There I also got a linear drift (but smaller) of 0.78 kJ/mol/ps<br>
>> (3.436*10^-5 kJ/mol/ps per atom).<br>
>> For comparison reasons I also did a NVT Nose-Hoover Simulation with<br>
>> manually set rlist=1.012nm:<br>
>> There I got a comparable linear drift of 0.67 kJ/mol/ps (2.94*10^-5<br>
>> kJ/mol/ps per atom).<br>
>> So no differences between NVE and NVT so far in my opinion...<br>
>><br>
>> Best,<br>
>> Bernhard<br>
>><br>
>> Am 15/07/15 um 17:10 schrieb Shirts, Michael R. (mrs5pt):<br>
>>> The conserved quantity in nose-hoover is not quite as good as the<br>
>>> conserved energy, which should have no drift at all. For NH, the<br>
>>> conserved quantity should drift as a random Gaussian process with mean<br>
>>> zero (i.e. go with sqrt(N)). It shouldn't be drifting linearly.<br>
>>><br>
>>> I would check to see if your system conserved energy when run with NVE<br>
>>> (use the endpoint of the NPT simulation). It's easier to diagnose any<br>
>>> problems with an NVE simulation, which should have virtually no<br>
>>> drift, vs<br>
>>> a NVT simulation, which has random noise drift. Odds are, if there<br>
>>> is a<br>
>>> problem with the NVT simulation, it will also show up in the NVE<br>
>>> simulation if only the thermostat is removed.<br>
>>><br>
>>> Also, consider looking at <a href="http://pubs.acs.org/doi/abs/10.1021/ct300688p" rel="noreferrer" target="_blank">http://pubs.acs.org/doi/abs/10.1021/ct300688p</a><br>
>>> for tests of whether the ensemble generated is correct.<br>
>>><br>
>>> Best,<br>
>>> ~~~~~~~~~~~~<br>
>>> Michael Shirts<br>
>>> Associate Professor<br>
>>> Department of Chemical Engineering<br>
>>> University of Virginia<br>
>>> <a href="mailto:michael.shirts@virginia.edu" target="_blank">michael.shirts@virginia.edu</a><br>
>>> (434) 243-1821<br>
>>><br>
>>><br>
>>><br>
>>> On 7/15/15, 10:58 AM, "Bernhard" <<a href="mailto:b.reuter@uni-kassel.de" target="_blank">b.reuter@uni-kassel.de</a>> wrote:<br>
>>><br>
>>>> Dear Gromacs Users and Developers,<br>
>>>><br>
>>>> I have a problem regarding energy conservation in my 10ns NVT<br>
>>>> protein+water+ions (22765 atoms) production (minimization and<br>
>>>> equilibration for more than 15ns was carried out in NPT before)<br>
>>>> simulations using a Nose-Hoover thermostat (tau=2.5ps).<br>
>>>> On first glance everything looks fine - the potential, kinetic and<br>
>>>> total<br>
>>>> energy are nearly perfectly constant (with normal fluctuations) - but<br>
>>>> when I checked the "Conserved-Energy" quantity that g_energy outputs I<br>
>>>> had to recognize a significant (nearly perfectly) linear downward<br>
>>>> drift<br>
>>>> of this "to-be-conserved" quantity of around 1.7 kJ/mol/ps (7.48*10^-5<br>
>>>> kJ/mol/ps per atom).<br>
>>>> This appears somehow disturbing to me since I would expect that this<br>
>>>> Conserved-Energy is the conserved energy of the extended Nose-Hoover<br>
>>>> Hamiltonian - which should by definition be conserved.<br>
>>>><br>
>>>> If it would be a drift caused by normal round-off error due to single<br>
>>>> precision I would expect it to grow with Sqrt(N) and not with N<br>
>>>> (linear)<br>
>>>> (N=number of steps).<br>
>>>> So I would like to know if this is a normal behaviour and also what<br>
>>>> could cause this (buffer size, precision, constraints etc)?<br>
>>>> Also I would like to know, if I am correct with my guess that the<br>
>>>> "Conserved-Energy" quantity is in this case the energy of the extended<br>
>>>> Nose-Hoover Hamiltonian?<br>
>>>> The .mdp file is atatched (don't be confused about rlist=1 - since Im<br>
>>>> using the Verlet-scheme the verlet-buffer-drift option should be by<br>
>>>> default active and determine the rlist value (Verlet buffer-size)<br>
>>>> automatically).<br>
>>>><br>
>>>> Best regards,<br>
>>>> Bernhard<br>
>>>><br>
>>>> ; Run parameters<br>
>>>> integrator = md ; leap-frog integrator<br>
>>>> nsteps = 10000000 ; 10000 ps = 10 ns<br>
>>>> dt = 0.001 ; 1 fs<br>
>>>> ; Output control<br>
>>>> nstxout = 5000 ; save coordinates every ps<br>
>>>> nstvout = 5000 ; save velocities every ps<br>
>>>> nstxtcout = 1000 ; xtc compressed trajectory output every ps<br>
>>>> nstenergy = 1000 ; save energies every ps<br>
>>>> nstlog = 5000 ; update log file every ps<br>
>>>> ; Bond parameters<br>
>>>> continuation = yes ; continue from NPT<br>
>>>> constraint_algorithm = lincs ; holonomic constraints<br>
>>>> constraints = h-bonds ; all bonds (even heavy atom-H bonds)<br>
>>>> constrained<br>
>>>> lincs_iter = 1 ; accuracy of LINCS<br>
>>>> lincs_order = 4 ; also related to accuracy<br>
>>>> ; Neighborsearching<br>
>>>> cutoff-scheme = Verlet ; Verlet cutoff-scheme instead of<br>
>>>> group-scheme (no charge-groups used)<br>
>>>> ns_type = grid ; search neighboring grid cells<br>
>>>> nstlist = 10 ; 10 fs<br>
>>>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br>
>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br>
>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br>
>>>> ; Electrostatics<br>
>>>> coulombtype = PME ; Particle Mesh Ewald for long-range<br>
>>>> electrostatics<br>
>>>> pme_order = 4 ; cubic interpolation<br>
>>>> fourierspacing = 0.12 ; grid spacing for FFT<br>
>>>> ; Temperature coupling is on<br>
>>>> tcoupl = nose-hoover ; modified Berendsen thermostat<br>
>>>> tc-grps = Protein Non-Protein ; two coupling groups - more<br>
>>>> accurate<br>
>>>> tau_t = 2.5 2.5 ; time constant, in ps<br>
>>>> ref_t = 300 300 ; reference temperature, one for each<br>
>>>> group, in K<br>
>>>> ; Pressure coupling is off<br>
>>>> pcoupl = no ; no pressure coupling in NVT<br>
>>>> ; Periodic boundary conditions<br>
>>>> pbc = xyz ; 3-D PBC<br>
>>>> ; Dispersion correction<br>
>>>> DispCorr = EnerPres ; account for cut-off vdW scheme<br>
>>>> ; Velocity generation<br>
>>>> gen_vel = no ; don¹t assign velocities from Maxwell<br>
>>>> distribution<br>
>>>><br>
>>>> --<br>
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>>>><br>
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>>>> posting!<br>
>>>><br>
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>>>> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br>
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</blockquote></div></div></div>