[gmx-users] temperature problem
Lovika Moudgil
lovikamoudgil at gmail.com
Thu Jun 4 14:52:26 CEST 2015
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
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
>>>>>>
>>>>>> * Please search the archive at
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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
>>>
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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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