[gmx-users] REMD - replicas sampling in temperatures beyond the assigned range
NISHA Prakash
nishnith20591 at gmail.com
Thu Jun 30 15:16:29 CEST 2016
Dear Justin,
Thank you for your reply.
It is a protein carbohydrate system. Including the solvent, the number of
atoms is 43499.
I have minimized the system for 200 ps followed by NPT and NVT simulations
for 200 ps respectively
Below is the .mdp file.
; VARIOUS PREPROCESSING OPTIONS
title = REMD Simulation
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = md-vv ; velocity verlet algorithm -
tinit = 0 ;
dt = 0.002 ; timestep in ps
nsteps = 5000000 ;
simulation-part = 1 ; Part index is updated automatically on
checkpointing
comm-mode = Linear ; mode for center of mass motion removal
nstcomm = 100 ; number of steps for center of mass motion
removal
comm-grps = Protein_Carb Water_and_Ions ; group(s) for
center of mass motion removal
; ENERGY MINIMIZATION OPTIONS
emtol = 10 ; Force tolerance
emstep = 0.01 ; initial step-size
niter = 20 ; Max number of iterations in relax-shells
fcstep = 0 ; Step size (ps^2) for minimization of
flexible constraints
nstcgsteep = 1000 ; Frequency of steepest descents steps when
doing CG
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
nstxout = 50000 ; Writing full precision coordinates every
ns
nstvout = 50000 ; Writing velocities every nanosecond
nstfout = 0 ; Not writing forces
nstlog = 5000 ; Writing to the log file every step 10ps
nstcalcenergy = 100
nstenergy = 5000 ; Writing out energy information every
step 10ps
nstxtcout = 2500 ; Writing coordinates every 5 ps
xtc-precision = 1000
xtc-grps = Protein_Carb Water_and_Ions ; subset of
atoms for the .xtc file.
energygrps = Protein_Carb Water_and_Ions ; Selection of
energy groups
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10 ; nblist update frequency-
ns-type = Grid ; ns algorithm (simple or grid)
pbc = xyz ; Periodic boundary conditions: xyz, no,
xy
periodic-molecules = no
rlist = 1.4 ; nblist cut-off
rlistlong = -1 ; long-range cut-off for switched
potentials
; OPTIONS FOR ELECTROSTATICS
coulombtype = PME ; Method for doing electrostatics
rcoulomb = 1.4 ;
epsilon-r = 1 ; Relative dielectric constant for the
medium
pme_order = 10;
; OPTIONS FOR VDW
vdw-type = Cut-off ; Method for doing Van der Waals
rvdw-switch = 0 ; cut-off lengths
rvdw = 1.4 ;
DispCorr = EnerPres; Apply long range dispersion
corrections for Energy and Pressure
table-extension = 1 ; Extension of the potential lookup tables
beyond the cut-off
fourierspacing = 0.08 ; Spacing for the PME/PPPM FFT grid
; GENERALIZED BORN ELECTROSTATICS
gb-algorithm = Still ; Algorithm for calculating Born radii
nstgbradii = 1 ; Frequency of calculating the Born radii
inside rlist
rgbradii = 1 ; Cutoff for Born radii calculation
gb-epsilon-solvent = 80 ; Dielectric coefficient of the implicit
solvent
gb-saltconc = 0 ; Salt concentration in M for Generalized
Born models
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = -1 ; Surface tension (kJ/mol/nm^2) for the SA
(nonpolar surface) part of GBSA - default -1
; Temperature coupling
tcoupl = nose-hoover
nsttcouple = 10 ;
nh-chain-length = 10
tc-grps = Protein_Carb Water_and_Ions ; Groups to
couple separately
tau-t = 10 10; Time constant (ps)-
ref-t = 270.0 270.0; reference temperature (K)
; pressure coupling
pcoupl = no ;-
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 270.0
gen-seed = 173529
; OPTIONS FOR BONDS
continuation = yes ; constrain the start configuration
constraints = all-bonds
constraint-algorithm = lincs ; Type of constraint algorithm-
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
Thank you for your help.
Nisha
On Thu, Jun 30, 2016 at 6:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/30/16 8:46 AM, NISHA Prakash wrote:
>
>> Dear all,
>>
>> I have conducted a 10ns REMD simulation for a protein ligand complex with
>> the temperature range - 270 to 350 K, however the temperature distribution
>> plot of the replicas show that the sampling has occurred at higher
>> temperatures as well that is beyond 350K -
>> Below is an excerpt from the temperature xvg file
>>
>>
>> @ title "Gromacs Energies"
>> @ xaxis label "Time (ps)"
>> @ yaxis label "(K)"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Temperature"
>> 0.000000 0.000000
>> 10.000000 350.997864
>> 20.000000 353.618927
>> 30.000000 350.068481
>> 40.000000 353.921753
>> 50.000000 359.485565
>> 60.000000 353.463654
>> 70.000000 352.015778
>> 80.000000 350.657898
>> 90.000000 351.927155
>> 100.000000 354.539429
>> 110.000000 354.287720
>> 120.000000 349.436096
>> 130.000000 352.960541
>> 140.000000 351.631317
>> 150.000000 354.217407
>> 160.000000 350.185852
>> 170.000000 350.294434
>> 180.000000 350.980194
>> 190.000000 350.914429
>> ....
>> ....
>> 470.000000 349.224060
>> 480.000000 350.819458
>> 490.000000 348.541748
>> 500.000000 350.393127
>> 510.000000 398.775208
>> 520.000000 444.802856
>> 530.000000 470.899323
>> 540.000000 466.652740
>> 550.000000 465.600677
>> 560.000000 469.225555
>> 570.000000 470.548370
>> 580.000000 470.011566
>> 590.000000 470.643951
>> 600.000000 472.433197
>> 610.000000 470.451172
>> 620.000000 469.991699
>> 630.000000 469.073090
>> 640.000000 467.259521
>> 650.000000 464.561798
>> 660.000000 468.416901
>> 670.000000 468.754913
>> 680.000000 469.259613
>> 690.000000 467.641144
>> 700.000000 468.542328
>>
>>
>> Temperature coupling was done using Nose hoover algorithm.
>>
>> Does this imply the sampling is wrong or insufficent?
>> Any help / suggestion is appreciated.
>>
>>
> How large is your system, and what is it? What were your (full) .mdp
> settings? The fact that your temperature started at 0 K and ramped up
> suggests that you did not equilibrate prior to the run, did not generate
> appropriate velocities, or did not continue properly. The sudden jump in
> temperature later suggests instability, and could be due to incorrect
> settings. N-H allows for large oscillations, but I wouldn't expect a
> stable system to that degree.
>
> -Justin
>
> --
> ==================================================
>
> 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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