[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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