[gmx-users] temperature problem
Lovika Moudgil
lovikamoudgil at gmail.com
Fri Jun 5 14:09:35 CEST 2015
Hi Justin... Yes I agree my system is behaving absurdly . But I am
wondering why !!I have done minimization without any error ..here is the
result ...
Steepest Descents converged to Fmax < 1000 in 1004 steps
Potential Energy = -9.6667906e+05
Maximum force = 9.7920349e+02 on atom 796
Norm of force = 1.7943926e+01
... I have One gold slab ...with golp parameters ..and amino acid on it
...in box with water and Na , Cl ions ....Freezing is for gold only....
System is not that big . And thing is temperature remain at the value (that
is 300K) for few time after some time it start behaving weird . If system
is wrong why its working even for one step ??
Thanks and Regards
Lovika
On Thu, Jun 4, 2015 at 6:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>>>>>>> posting!
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>>>>>>>> --
>>>>>>>>
>>>>>>> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>> --
>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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