[gmx-users] Is anyone also using lammps?s
Peng Yi
pengyi at MIT.EDU
Wed Nov 4 14:55:29 CET 2009
Hi, Ran,
No, I haven't. I still have to find out how to install in double
precision. Would double precision be slower than single? If so,
how much? Or just double the memory used? Thanks,
-Peng
On Wed, 4 Nov 2009, Ran Friedman wrote:
> Dear Peng,
>
> Did you also try to run GMX in double precision at some point?
>
> Ran
>
> Peng Yi wrote:
>>
>> I turned off the torsion interaction. The difference between Lammps
>> and Gromacs at integration time step 2fs was reduced. Details below:
>>
>> A melt of 240 n-octane (united-atom model), NVT, T=300K, V=55.46nm^3.
>> Both Lammps and Gromacs use berendsen thermostat with tau_t=1ps.
>>
>> Integration time step 1fs:
>> Lammps Gromacs Std. Err. (for both)
>> Ebond(kJ/mol): 2092 2109 100
>> Eangle: 1778 1754 80
>> Elj+corr: -10501 -10553 100
>> T(K): 300 299 5
>> P(atm): 3188 3016 700
>>
>> integration time step 2fs:
>> Lammps Gromacs Std.Err. (for both)
>> Ebond: 2133 2232 100
>> Eangle: 1803 1737 80
>> Elj+corr: -10501 -10623 100
>> T: 300 298 5
>> P: 3133 2955 600
>>
>> Lammps results remain almost unchanged when dt increases from 1fs to 2fs,
>> and Ebond : Eangle = 7 : 6, which is the ratio between # of bonds and
>> # of angles.
>>
>> Gromacs results change more significantly when dt goes from 1fs to 2fs.
>> and the trend of Ebond and Eangle are opposite. It is more significant
>> when torsion interaction is present.
>>
>>
>> On Tue, 3 Nov 2009, David van der Spoel wrote:
>>
>>> Peng Yi wrote:
>>>>
>>>> Hi, David,
>>>>
>>>> I used Berendsen thermostat and a bigger tau_t=1ps to redo the
>>>> simulations.
>>>> The general conclusion is the same. The std err is the same in both
>>>> packages. And during each simulation, the integration time does not
>>>> change. Details below:
>>>>
>>>> Integration time step 1fs:
>>>> Lammps Gromacs Std.Err. (for both)
>>>> Ebond(kJ/mol): 2112 2170 100
>>>> Eangle: 1799 1770 100
>>>> Etors: 2552 2490 100
>>>> Elj+corr: -10711 -10777 100
>>>> P(atm): 3250 3216 500
>>>>
>>>> Integration time step 2fs:
>>>> Lammps Gromacs Std.Err. (for both)
>>>> Ebond: 2154 2654 120
>>>> Eangle: 1840 1645 120
>>>> Etors: 2573 2236 120
>>>> Elj+corr: -10711 -11019 100 P(atm):
>>>> 3250 2590 600
>>>>
>>>
>>> How about the temperature in both systems? Was Lammps also run with
>>> Berendsen? It could also still be a topology error. Maybe you can
>>> turn off the torsion potential to test this.
>>>
>>>> -Peng
>>>>
>>>> On Sun, 1 Nov 2009, David van der Spoel wrote:
>>>>
>>>>> Peng Yi wrote:
>>>>>>
>>>>>> Thank for your reply! I have done some NVT runs per your
>>>>>> suggestion, and
>>>>>> the results are similar to NPT runs, i.e., Gromacs results is more
>>>>>> affected by changing integration timestep than Lammps. Details
>>>>>> below:
>>>>>>
>>>>>> A melt of 240 octane chains by united-atom model. T=300K, V=55.46
>>>>>> nm^3.
>>>>>> Both Gromacs and Lammps use Nose-Hoover thermostat with tau_t=0.2 ps.
>>>>>
>>>>> As some people have note the tau_t is short for Nose Hoover. Are
>>>>> you sure this means the same in Lammps and in Gromacs? For one
>>>>> thing, there is no tau_t in the NH algorithm as far as I know, and
>>>>> Gromacs converts it to an appropriate weight or whatever that is
>>>>> called. What does Lammps do with this tau_t. To be a the safe side
>>>>> you could run both with Berendsen as well. Is the std err identical
>>>>> in both packages? And in the 2 fs run, are both simulation
>>>>> equlibrated with this time step as well?
>>>>>
>>>>>> All other parameters in .top and .mdp files are the same as
>>>>>> previously
>>>>>> attached..
>>>>>>
>>>>>> If I use integration time 1fs, Lammps and Gromacs produce
>>>>>> consistent results:
>>>>>> Lammps Gromacs std. err.
>>>>>> Ebond(kJ/mol): 2133 2160 100
>>>>>> Eangle: 1757 1780 80
>>>>>> Etors: 2531 2510 80
>>>>>> Elj+corr: -10711 -10767 90
>>>>>> P(atm): 3500 3250 500
>>>>>>
>>>>>> if I use integration time 2fs, Lammps results remain unchanged, but
>>>>>> Gromacs results change significantly, particularly bonded energy:
>>>>>>
>>>>>> Lammps Gromacs std. err.
>>>>>> Ebond(kJ/mol): 2175 2710 100
>>>>>> Eangle: 1799 1640 70
>>>>>> Etors: 2573 2230 80
>>>>>> Elj+corr: -10711 -11007 100 P(atm):
>>>>>> 3200 2730 700
>>>>>>
>>>>>> Would that be a result of using different integrator between
>>>>>> Lammps and Gromacs? Lammps uses Velocity-Verlet, and Gromacs uses
>>>>>> Leap-frog.
>>>>>> Thanks,
>>>>>> -Peng
>>>>>>
>>>>>> On Thu, 29 Oct 2009, David van der Spoel wrote:
>>>>>>
>>>>>>> aherz wrote:
>>>>>>>> Hey,
>>>>>>>>
>>>>>>>> are you running single or double precision gromacs?
>>>>>>>> Afaik, depending on the circumstances the energy drift in
>>>>>>>> gromacs can be
>>>>>>>> rather bad for single precision.
>>>>>>>
>>>>>>> Please refer to the gromacs 4.0 paper for a discussion of the drift.
>>>>>>> If you want to compare energies you need the same density, which
>>>>>>> you do not have, you may need to run NVT for that.
>>>>>>>
>>>>>>> Note that your integration time step is quite large, and the
>>>>>>> temperature coupling constant is very small.
>>>>>>>
>>>>>>> You could try a shifted LJ + dispersion correction, it is not
>>>>>>> clear to me how LAMMPS treats cutoffs, couldn't find it in the
>>>>>>> manual.
>>>>>>>
>>>>>>>>
>>>>>>>> Alex
>>>>>>>>
>>>>>>>>
>>>>>>>> Peng Yi schrieb:
>>>>>>>>> On Wed, 28 Oct 2009, Mark Abraham wrote:
>>>>>>>>>
>>>>>>>>>> Peng Yi wrote:
>>>>>>>>>>> I am trying to simulate alkane melt and found out that
>>>>>>>>>>> gromacs and
>>>>>>>>>>> lammps gave different results, particularly the bonded
>>>>>>>>>>> interaction
>>>>>>>>>>> energy.
>>>>>>>>>>> I wonder if anyone has such experience. Thanks,
>>>>>>>>>> Even two installations of the same version of GROMACS can give
>>>>>>>>>> different results. The question is whether when using comparable
>>>>>>>>>> model physics you observe the same ensemble averages.
>>>>>>>>>>
>>>>>>>>>> Mark
>>>>>>>>> Hi, Mark,
>>>>>>>>>
>>>>>>>>> Thanks for reply! The difference is statistically
>>>>>>>>> significant. And I am
>>>>>>>>> wondering if it is caused by the integrator: Leap-frog for
>>>>>>>>> Gromacs and
>>>>>>>>> Velocity-verlet for Lammps. Detail description of the
>>>>>>>>> comparison please
>>>>>>>>> see below:
>>>>>>>>>
>>>>>>>>> It is an NPT simulation of a melt of 240 n-octane molecules using
>>>>>>>>> united-atom model, i.e., CHx group is considered as one atom.
>>>>>>>>> There are
>>>>>>>>> bond, angle, torsion and LJ interactions. T=300K and P=1atm.
>>>>>>>>>
>>>>>>>>> Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
>>>>>>>>> nose-hoover thermostat and Parranello-Rahman barostat. Time
>>>>>>>>> constants
>>>>>>>>> for
>>>>>>>>> thermostat and barostat are 0.02ps and 2.0ps, respectively.
>>>>>>>>>
>>>>>>>>> If I use integration time 1fs, Lammps and Gromacs gave consistent
>>>>>>>>> results:
>>>>>>>>> Lammps Gromacs
>>>>>>>>> Ebond(kJ/mol): 2092 2146
>>>>>>>>> Eangle: 1757 1760
>>>>>>>>> Etors: 2510 2500
>>>>>>>>> Elj+corr: -9238 -9350
>>>>>>>>> Volume(nm^3): 66.7 66.5
>>>>>>>>>
>>>>>>>>> where energy fluctuation is 100 kJ/mol and volume fluctuation
>>>>>>>>> is 1 nm^3,
>>>>>>>>> Elj+corr is the total LJ energy including tail correction.
>>>>>>>>>
>>>>>>>>> However, if I use integration time 2fs, Lammps results do not
>>>>>>>>> change
>>>>>>>>> much, but Gromacs results changed a lot:
>>>>>>>>>
>>>>>>>>> Lammps Gromacs
>>>>>>>>> Ebond(kJ/mol): 2133 2700
>>>>>>>>> Eangle: 1799 1640
>>>>>>>>> Etors: 2552 2200
>>>>>>>>> Elj+corr: -9292 -9886
>>>>>>>>> Volume: 66.7 64.0
>>>>>>>>>
>>>>>>>>> The results given by Lammps is more reasonable because the
>>>>>>>>> Ebond should
>>>>>>>>> be equal to the total # of bonds times 1/2k_BT and Eangle
>>>>>>>>> should be equal
>>>>>>>>> to the total # of angles times 1/2k_BT. At T=300K,
>>>>>>>>> 1/2k_BT=1.25 kJ/mol.
>>>>>>>>> 240 n-octanes have total 1680 bonds and 1440 angles.
>>>>>>>>>
>>>>>>>>> The bond and angle interactions are both harmonic functions. Bond
>>>>>>>>> interaction constant kl=292880 kJ/mol/nm^2, corresponding to a
>>>>>>>>> bond
>>>>>>>>> ossilation period 16 fs.
>>>>>>>>>
>>>>>>>>> Is there something related to the integrator?
>>>>>>>>>
>>>>>>>>> Here I attached my grompp.mdp and topol.top files.
>>>>>>>>>
>>>>>>>>> ##########
>>>>>>>>> grompp.mdp
>>>>>>>>> ##########
>>>>>>>>>
>>>>>>>>> ; VARIOUS PREPROCESSING OPTIONS
>>>>>>>>> title = Yo
>>>>>>>>> cpp = /usr/bin/cpp
>>>>>>>>> include = define =
>>>>>>>>>
>>>>>>>>> ; RUN CONTROL PARAMETERS
>>>>>>>>> integrator = md
>>>>>>>>> tinit = 0
>>>>>>>>> dt = 0.001
>>>>>>>>> nsteps = 2000000
>>>>>>>>> init_step = 0
>>>>>>>>> comm-mode = Linear
>>>>>>>>> nstcomm = 1
>>>>>>>>> comm-grps =
>>>>>>>>>
>>>>>>>>> ; OUTPUT CONTROL OPTIONS
>>>>>>>>> nstxout = 5000
>>>>>>>>> nstvout = 5000
>>>>>>>>> nstfout = 5000
>>>>>>>>> nstcheckpoint = 10000
>>>>>>>>> nstlog = 1000
>>>>>>>>> nstenergy = 1000
>>>>>>>>> nstxtcout = 5000
>>>>>>>>> xtc-precision = 1000
>>>>>>>>> xtc-grps = energygrps =
>>>>>>>>>
>>>>>>>>> ; NEIGHBORSEARCHING PARAMETERS
>>>>>>>>> nstlist = 10
>>>>>>>>> ns_type = grid
>>>>>>>>> pbc = xyz
>>>>>>>>> rlist = 1.0025
>>>>>>>>> domain-decomposition = no
>>>>>>>>>
>>>>>>>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>>>>>>>> coulombtype = Cut-off
>>>>>>>>> rcoulomb-switch = 0
>>>>>>>>> rcoulomb = 1.0025
>>>>>>>>> epsilon-r = 1
>>>>>>>>> vdw-type = Cut-off
>>>>>>>>> rvdw-switch = 0 ; default rvdw = 1.0025
>>>>>>>>> ; default 1 nm
>>>>>>>>> DispCorr = EnerPres
>>>>>>>>> ;table-extension = 1.5
>>>>>>>>> fourierspacing = 0.12
>>>>>>>>> fourier_nx = 0
>>>>>>>>> fourier_ny = 0
>>>>>>>>> fourier_nz = 0
>>>>>>>>> pme_order = 4
>>>>>>>>> ewald_rtol = 1e-05
>>>>>>>>> ewald_geometry = 3d
>>>>>>>>> epsilon_surface = 0
>>>>>>>>> optimize_fft = no
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>>>>>>>>> Tcoupl = nose-hoover
>>>>>>>>> tc-grps = System
>>>>>>>>> tau_t = 0.02
>>>>>>>>> ref_t = 300.0
>>>>>>>>> Pcoupl = Parrinello-Rahman
>>>>>>>>> Pcoupltype = isotropic
>>>>>>>>> tau_p = 2.0
>>>>>>>>> compressibility = 4.5e-5
>>>>>>>>> ref_p = 1.0
>>>>>>>>> andersen_seed = 815131
>>>>>>>>>
>>>>>>>>> ; GENERATE VELOCITIES FOR STARTUP RUN
>>>>>>>>> gen_vel = yes
>>>>>>>>> gen_temp = 300
>>>>>>>>> gen_seed = 2009
>>>>>>>>>
>>>>>>>>> ; OPTIONS FOR BONDS constraints = none
>>>>>>>>> constraint-algorithm = Lincs
>>>>>>>>> unconstrained-start = no
>>>>>>>>> Shake-SOR = no
>>>>>>>>> shake-tol = 1e-04
>>>>>>>>> lincs-order = 4
>>>>>>>>> lincs-iter = 1
>>>>>>>>> lincs-warnangle = 30
>>>>>>>>> morse = no
>>>>>>>>>
>>>>>>>>> ; ENERGY GROUP EXCLUSIONS
>>>>>>>>> ; Pairs of energy groups for which all non-bonded interactions are
>>>>>>>>> excluded
>>>>>>>>> energygrp_excl =
>>>>>>>>>
>>>>>>>>> ; NMR refinement stuff disre = No
>>>>>>>>> disre-weighting = Conservative
>>>>>>>>> disre-mixed = no
>>>>>>>>> disre-fc = 1000
>>>>>>>>> disre-tau = 0
>>>>>>>>> nstdisreout = 100
>>>>>>>>> orire = no
>>>>>>>>> orire-fc = 0
>>>>>>>>> orire-tau = 0
>>>>>>>>> orire-fitgrp = nstorireout = 100
>>>>>>>>> dihre = No
>>>>>>>>> dihre-fc = 1000
>>>>>>>>> dihre-tau = 0
>>>>>>>>> nstdihreout = 100
>>>>>>>>>
>>>>>>>>> #########
>>>>>>>>> topol.top
>>>>>>>>> #########
>>>>>>>>>
>>>>>>>>> #include "ffG53a6.itp"
>>>>>>>>>
>>>>>>>>> [atom-types]
>>>>>>>>> ;name mass charge ptype V/c6 W/c12
>>>>>>>>> CH2 14.0 0.00 A 0.0 0.0
>>>>>>>>> CH3 15.0 0.00 A 0.0 0.0
>>>>>>>>>
>>>>>>>>> [nonbond-params]
>>>>>>>>> ; i j func V/c6 W/c12
>>>>>>>>> CH2 CH2 1 0.0078 3.24e-5
>>>>>>>>> CH2 CH3 1 0.0078 3.24e-5
>>>>>>>>> CH3 CH3 1 0.0078 3.24e-5
>>>>>>>>>
>>>>>>>>> [ moleculetype ]
>>>>>>>>> ; name nrexcl
>>>>>>>>> Octane1 3
>>>>>>>>>
>>>>>>>>> [ atoms ]
>>>>>>>>> ; nr type resnr residu atom cgnr charge
>>>>>>>>> 1 CH3 1 C8 CH3 1 0.0
>>>>>>>>> 2 CH2 1 C8 CH2 2 0.0
>>>>>>>>> 3 CH2 1 C8 CH2 3 0.0
>>>>>>>>> 4 CH2 1 C8 CH2 4 0.0
>>>>>>>>> 5 CH2 1 C8 CH2 5 0.0
>>>>>>>>> 6 CH2 1 C8 CH2 6 0.0
>>>>>>>>> 7 CH2 1 C8 CH2 7 0.0
>>>>>>>>> 8 CH3 1 C8 CH3 8 0.0
>>>>>>>>>
>>>>>>>>> [ bonds ]
>>>>>>>>> ; ai aj funct c0(nm) c1(kJ/mol/nm^2)
>>>>>>>>> 1 2 1 0.153 292880.0
>>>>>>>>> 2 3 1 0.153 292880.0
>>>>>>>>> 3 4 1 0.153 292880.0
>>>>>>>>> 4 5 1 0.153 292880.0
>>>>>>>>> 5 6 1 0.153 292880.0
>>>>>>>>> 6 7 1 0.153 292880.0
>>>>>>>>> 7 8 1 0.153 292880.0
>>>>>>>>>
>>>>>>>>> [ pairs ]
>>>>>>>>> ; ai aj funct c0 c1
>>>>>>>>> ; 1 4 1 0.000000e+00 0.000000e+00 ; 2 5 1
>>>>>>>>> 0.000000e+00 0.000000e+00 ; 3 6 1 0.000000e+00
>>>>>>>>> 0.000000e+00
>>>>>>>>> ; 4 7 1 0.000000e+00 0.000000e+00 ; 5 8 1
>>>>>>>>> 0.000000e+00 0.000000e+00
>>>>>>>>>
>>>>>>>>> [ angles ]
>>>>>>>>> ; ai aj ak funct c0(degree) c1(kJ/mol/rad^-2)
>>>>>>>>> 1 2 3 1 109.5 502.08
>>>>>>>>> 2 3 4 1 109.5 502.08
>>>>>>>>> 3 4 5 1 109.5 502.08
>>>>>>>>> 4 5 6 1 109.5 502.08
>>>>>>>>> 5 6 7 1 109.5 502.08
>>>>>>>>> 6 7 8 1 109.5 502.08
>>>>>>>>>
>>>>>>>>> [ dihedrals ]
>>>>>>>>> ; ai aj ak al funct c0 c1 c2
>>>>>>>>> c3 c4 c5
>>>>>>>>> 1 2 3 4 3 6.4977 16.9868 3.6275
>>>>>>>>> -27.112 0 0
>>>>>>>>> 2 3 4 5 3 6.4977 16.9868 3.6275
>>>>>>>>> -27.112 0 0
>>>>>>>>> 3 4 5 6 3 6.4977 16.9868 3.6275
>>>>>>>>> -27.112 0 0
>>>>>>>>> 4 5 6 7 3 6.4977 16.9868 3.6275
>>>>>>>>> -27.112 0 0
>>>>>>>>> 5 6 7 8 3 6.4977 16.9868 3.6275
>>>>>>>>> -27.112 0 0
>>>>>>>>>
>>>>>>>>> [ system ]
>>>>>>>>> octane melt
>>>>>>>>>
>>>>>>>>> [ molecules ]
>>>>>>>>> Octane1 240
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> David.
>>>>>>> ________________________________________________________________________
>>>>>>> David van der Spoel, PhD, Professor of Biology
>>>>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>>>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>>>>>> phone: 46 18 471 4205 fax: 46 18 511 755
>>>>>>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>>>> _______________________________________________
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>>>>>
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>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
>>> +4618511755.
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