[gmx-users] temperature problem
Justin Lemkul
jalemkul at vt.edu
Thu Jun 4 14:57:46 CEST 2015
On 6/4/15 8:52 AM, Lovika Moudgil wrote:
> Hiii....Here is my .mdp file below ...
>
> title = OPLS Lysozyme NVT equilibration
> define = -DPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 2000000 ; 2 * 50000 = 100 ps
> dt = 0.001 ; 2 fs
> ; Output control
> nstxout = 500 ; save coordinates every 1.0 ps
> nstvout = 500 ; save velocities every 1.0 ps
> nstenergy = 500 ; save energies every 1.0 ps
> nstlog = 500 ; update log file every 1.0 ps
> nstxtcout = 500 ; [steps] freq to write coordinates
> to xtc trajectory
> xtc_precision = 1000 ; [real] precision to write xtc
> trajectory
> comm_mode = Linear
> comm_grps = Protein Non-Protein ; group(s) for center of
> mass motion removal
> ; Bond parameters
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy
> atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; 7.3.9 Neighbor Searching
> cutoff-scheme = Verlet
> nstlist = 10 ; [steps] freq to update neighbor
> list
> ns_type = grid ; method of updating neighbor list
> pbc = xyz ; periodic boundary conditions in
> all directions
> rlist = 1.0 ; [nm] cut-off distance for the
> short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype = PME ; Particle-Mesh Ewald electrostatics
> rcoulomb = 1.0 ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> rvdw = 1.0 ; [nm] distance for LJ cut-off
> DispCorr = Ener ; apply long range dispersion
> corrections
>
> ; 7.3.13 Ewald
> fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
> when using PME
> pme_order = 4 ; interpolation order for PME, 4 =
> cubic
> ewald_rtol = 1e-5 ; relative strength of
> Ewald-shifted potential at rcoulomb
> ; Temperature coupling is on
> tcoupl = nose-hoover ; modified Berendsen thermostat
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one for each
> group, in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
> ; To keep au surface in place, freeze Au atoms.
> ; The AU group has been defined via make_ndx
> ; to contains all the AU atoms ('a AU').
> freezegrps = AUS AUB AUI
> freezedim = Y Y Y Y Y Y Y Y Y
>
>
> And in one part of log file.... temperature is getting high..without error
> ....and it keeps on increasing ...
>
> Energies (kJ/mol)
> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
> 2.91339e+01 3.23884e-01 8.52437e+00 1.65299e+01 2.68992e+02
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 5.70551e+05 -6.29186e+03 -8.96225e+05 4.42542e+03 -3.27216e+05
> Kinetic En. Total Energy Conserved En. *Temperature* Pres. DC
> (bar)
> 9.71936e+09 9.71903e+09 2.71970e+19 * 2.35145e+07*
> 0.00000e+00
Ask yourself whether or not this is even reasonable. A temperature of 10^7?
That's 4000x hotter than the surface of the sun. There's no way that's real.
Your system is physically nonsensical. You'll have to describe in complete
detail what it is you're trying to do, but the combination of multiple
comm-grps, freezing (which is a pretty massive perturbation in and of itself),
restraints, etc. is quite complex and any number of things could be causing a
problem. It could be something as simple as insufficient minimization and/or
bad starting coordinates in general, but it's a shot in the dark at this point.
-Justin
> Pressure (bar) Constr. rmsd
>
> Thanks and Regards
> Lovika
>
> On Thu, Jun 4, 2015 at 5:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/4/15 12:39 AM, Lovika Moudgil wrote:
>>
>>> Hi...Justin.... Thanks for explaining ...... I just want to ask could
>>> there be any other reasons too?? ...Because I have tried it with PME
>>> too...and still I am not getting desired temperature ....
>>>
>>>
>> You'll have to provide a full .mdp file and quantitative evidence of what
>> you're seeing. There are plenty of things that could be going on, but I'm
>> not going just blindly guess.
>>
>>
>> -Justin
>>
>>
>>>
>>> Thanks and Regards
>>> Lovika
>>>
>>>
>>> On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 6/3/15 3:46 AM, Lovika Moudgil wrote:
>>>>
>>>> Hi...thanks for reply Peter and Mark ....I tried with temperature
>>>>> coupling
>>>>> . But things are still same ...
>>>>>
>>>>> Hi ... Mark would you like to explain this factor to me ??
>>>>>
>>>>>
>>>>> Using a plain cutoff in the condensed phase is outdated methodology
>>>> that
>>>> is very inaccurate. Cutoff artifacts lead to accumulation of heat in the
>>>> system. Use something sensible like PME.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> Thanks and Regards
>>>>
>>>>> Lovika
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> Runaway heating is the only useful feature of cutoff electrostatics.
>>>>>> Use
>>>>>> an
>>>>>> actual model physics.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon <p.c.kroon at rug.nl> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 02/06/15 09:43, Lovika Moudgil wrote:
>>>>>>>
>>>>>>> Hi everyone
>>>>>>>>
>>>>>>>>
>>>>>>>> I am having some problem in my md run .In my system temperature of
>>>>>>>>
>>>>>>>> system
>>>>>>>
>>>>>>
>>>>>> is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
>>>>>>>
>>>>>>>>
>>>>>>>> using
>>>>>>>
>>>>>>> it for further md simulation .I am not getting any error for this
>>>>>>>> temperature increase .....But when I plot temperature graph ,
>>>>>>>>
>>>>>>>> temperature
>>>>>>>
>>>>>>
>>>>>> is not same as nvt and is very high in md .I am having gold slab and
>>>>>>>
>>>>>>>>
>>>>>>>> amino
>>>>>>>
>>>>>>> acid in my system . Mdp file for md run is below ....Is their any
>>>>>>>> error
>>>>>>>>
>>>>>>>> in
>>>>>>>
>>>>>>> my mdp file ???what could be the reason for this ???Please suggest
>>>>>>>> ....
>>>>>>>> ; Run parameters
>>>>>>>> integrator = md ; leap-frog integrator
>>>>>>>> nsteps = 30000000 ; 2 * 50000 = 100 ps
>>>>>>>> dt = 0.001 ; 2 fs
>>>>>>>> ; Output control
>>>>>>>> ; Output control
>>>>>>>> nstxout = 500 ; save coordinates every 1.0 ps
>>>>>>>> nstvout = 500 ; save velocities every 1.0 ps
>>>>>>>> nstenergy = 500 ; save energies every 1.0 ps
>>>>>>>> nstlog = 500 ; update log file every 1.0 ps
>>>>>>>> nstxtcout = 500 ; [steps] freq to write
>>>>>>>>
>>>>>>>> coordinates
>>>>>>>
>>>>>>> to xtc trajectory
>>>>>>>> xtc_precision = 1000 ; [real] precision to write
>>>>>>>> xtc
>>>>>>>> trajectory
>>>>>>>> xtc_grps = System ; group(s) to write to xtc
>>>>>>>> trajectory
>>>>>>>> energygrps = System ; group(s) to write to energy
>>>>>>>>
>>>>>>>> file
>>>>>>>
>>>>>>> ; Bond parameters
>>>>>>>>
>>>>>>>> constraint_algorithm = lincs ; holonomic constraints
>>>>>>>> constraints = all-bonds ; all bonds (even heavy
>>>>>>>> atom-H bonds) constrained
>>>>>>>> lincs_iter = 1 ; accuracy of LINCS
>>>>>>>> lincs_order = 4 ; also related to accuracy
>>>>>>>> ; Neighborsearching
>>>>>>>> cutoff-scheme = Verlet
>>>>>>>> ns_type = grid ; search neighboring grid cells
>>>>>>>> nstlist = 10 ; 20 fs, largely irrelevant with
>>>>>>>> Verlet
>>>>>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in
>>>>>>>> nm)
>>>>>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in
>>>>>>>> nm)
>>>>>>>>
>>>>>>>> ; Electrostatics
>>>>>>>> coulombtype = cut-off
>>>>>>>> pme_order = 4 ; cubic interpolation
>>>>>>>> fourierspacing = 0.12 ; grid spacing for FFT
>>>>>>>> ; Temperature coupling is on
>>>>>>>> tcoupl = nose-hoover ; modified Berendsen
>>>>>>>>
>>>>>>>> thermostat
>>>>>>>
>>>>>>> tc-grps = Protein AUS AUB AUI SOL NA CL ; two coupling
>>>>>>>>
>>>>>>>> groups -
>>>>>>>
>>>>>>
>>>>>> more accurate
>>>>>>>
>>>>>>>> tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time
>>>>>>>> constant,
>>>>>>>>
>>>>>>>> in ps
>>>>>>>
>>>>>>> ref_t = 300 300 300 300 300 300 300 ; reference
>>>>>>>> temperature, one for each group, in K
>>>>>>>>
>>>>>>>> You have too many temperature coupling groups. (What Not To Do on
>>>>>>> http://www.gromacs.org/Documentation/Terminology/Thermostats)
>>>>>>> I'd stick to one for proteins, and one for the rest.
>>>>>>>
>>>>>>> ; Pressure coupling is off
>>>>>>>> pcoupl = no ; no pressure coupling in NVT
>>>>>>>> ; Periodic boundary conditions
>>>>>>>> pbc = xyz ; 3-D PBC
>>>>>>>> ; Dispersion correction
>>>>>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>>>>>> ; Velocity generation
>>>>>>>> ; Velocity generation
>>>>>>>> gen_vel = yes ; assign velocities from Maxwell
>>>>>>>>
>>>>>>>> distribution
>>>>>>>
>>>>>>
>>>>>> gen_temp = 300 ; temperature for Maxwell distribution
>>>>>>>
>>>>>>>> gen_seed = -1 ; generate a random seed
>>>>>>>>
>>>>>>>> ; To keep au surface in place, freeze Au atoms.
>>>>>>>> ; The AU group has been defined via make_ndx
>>>>>>>> ; to contains all the AU atoms ('a AU').
>>>>>>>> freezegrps = AUS AUB AUI
>>>>>>>> freezedim = Y Y Y Y Y Y Y Y Y
>>>>>>>> comm_mode = None
>>>>>>>>
>>>>>>>> Thanks and Reagrds
>>>>>>>> Lovika
>>>>>>>>
>>>>>>>>
>>>>>>> Peter
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
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>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>>
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>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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