[gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
changwoonjang at gmail.com
Tue Jan 5 20:57:56 CET 2016
Dear Justin,
The following is from .mdf file.
; VARIOUS PREPROCESSING OPTIONS
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 22500000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1000
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 1
emstep = 0.01
; Max number of iterations in relax_shells
niter = 200
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 0
nstfout = 1000
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.22
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb-switch = 0
rcoulomb = 1.22
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.22
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.26
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = no
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = v-rescale
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 1.0
ref_t = 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
gen_vel = yes
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
On Tue, Jan 5, 2016 at 2:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/5/16 2:51 PM, Chang Woon Jang wrote:
>
>> Dear Justin,
>>
>> Please take a look at the file. I modified mdp file provided from VOTCA
>> tutorial. I think that mdp file is ok.
>>
>>
> The mailing list does not accept attachments. Copy and paste the .mdp
> contents.
>
> -Justin
>
>
> Thank you very much.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang <changwoonjang at gmail.com>
>> wrote:
>>
>> Dear Justin,
>>>
>>> Please take a look at the files. I modified mdp file provided from
>>> VOTCA
>>> tutorial. I think that mdp file is ok.
>>>
>>> I also attached full topology files as well.
>>>
>>> Thank you very much.
>>>
>>> Best regards,
>>> Changwoon Jang
>>>
>>>
>>> On Tue, Jan 5, 2016 at 2:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 1/5/16 2:25 PM, Chang Woon Jang wrote:
>>>>
>>>> Dear Justin,
>>>>>
>>>>> I am curious about resizing the box. My system contains 15000
>>>>> atoms
>>>>> representing liquid polymer with very low density (maybe gas phase due
>>>>> to
>>>>> very low density). Does this very low density affect the simulation not
>>>>> to
>>>>> converge the box? Or, do the initial conditions (Pcoupl=berendsen,
>>>>> Pcoupltype=isotropic, tau_p=5.0, compressibility=4.5e-5, ref_p=1.0) in
>>>>> gromapp.mdp affect? Do I need to test these conditions? I am just
>>>>> starting
>>>>> to use GROMACS for obtaining atomistic trajectory compatible with VOTCA
>>>>> coarse-graining package.
>>>>>
>>>>>
>>>>> Those settings should be fine. Extract the box vectors from the .edr
>>>> file and see how much they fluctuate; the final snapshot is not
>>>> necessarily
>>>> representative. But the fact that the box size is exactly the same from
>>>> start to finish suggests there is something incorrect (or at least,
>>>> really
>>>> weird) going on. Provide the full text of your .mdp please, not just
>>>> the
>>>> section you think is relevant.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> The same configuration in LAMMPS works fine.
>>>>
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Best regards,
>>>>> Changwoon Jang
>>>>>
>>>>> On Tue, Jan 5, 2016 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 1/5/16 1:42 PM, Chang Woon Jang wrote:
>>>>>>
>>>>>> Dear Abhishek Khetan,
>>>>>>
>>>>>>>
>>>>>>> Thank you for your answer. It means that Gromacs does not
>>>>>>> automatically
>>>>>>> adjust the box size even though NPT ensemble is employed. Am I right?
>>>>>>>
>>>>>>>
>>>>>>> This is incorrect. The box size will change under the influence of
>>>>>>>
>>>>>> pressure. Its shape should be conserved. But if you're seeing the
>>>>>> exact
>>>>>> same box vectors before and after the simulation, something went wrong
>>>>>> with
>>>>>> your input.
>>>>>>
>>>>>> Different from Gromacs, Lammps automatically adjust box size when NPT
>>>>>>
>>>>>> ensemble is applied during the simulation. Therefore, the density is
>>>>>>> able
>>>>>>> to be fitted with initial conditions (pressure, temperature,
>>>>>>> simulation
>>>>>>> time).
>>>>>>>
>>>>>>>
>>>>>>> GROMACS does this, too.
>>>>>>>
>>>>>>
>>>>>> When I used the "gmx editconf" to resize the box to correct a density,
>>>>>> vmd
>>>>>>
>>>>>> shows a very ugly configurations. I think that topology file will
>>>>>>> check
>>>>>>> the
>>>>>>> bond informations no matter how the gro file, containing only atom
>>>>>>> coordinates and box size, looks like.
>>>>>>>
>>>>>>>
>>>>>>> Indeed, editconf is not useful here. It scales coordinate positions
>>>>>>> to
>>>>>>>
>>>>>> achieve the desired density. This is not what you want.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>> If I am wrong, please correct me.
>>>>>>
>>>>>>
>>>>>>> Thank you.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Changwoon Jang
>>>>>>>
>>>>>>> On Tue, Jan 5, 2016 at 1:16 PM, abhishek khetan <askhetan at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>> To rescale the box.gro to a desired size using the actual density
>>>>>>> 543.21
>>>>>>>
>>>>>>> kg/l of the solvent and get a new scaled.gro file, I use this
>>>>>>>> command:
>>>>>>>>
>>>>>>>> $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang <
>>>>>>>> changwoonjang at gmail.com
>>>>>>>>
>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>
>>>>>>>> Dear Gromacs Users,
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> I have a low density polymer system initially. I would like to fit
>>>>>>>>> the
>>>>>>>>> correct liquid density using NPT simulation.
>>>>>>>>>
>>>>>>>>> I used Pcoupl=berendsen for 22 ns but the box size in confout.gro
>>>>>>>>> is
>>>>>>>>>
>>>>>>>>> still
>>>>>>>>>
>>>>>>>>
>>>>>>>> the same as the input size of conf.gro.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Initial in conf.gro (10.0 10.0 9.8)
>>>>>>>>> output in confout.gro (10.0 10.0 9.8)
>>>>>>>>>
>>>>>>>>> My initial conditions are
>>>>>>>>>
>>>>>>>>> tau_p=5.0
>>>>>>>>> compressibility=4.5e-5
>>>>>>>>> ref_p=1.0
>>>>>>>>>
>>>>>>>>> Do I need to increase compressibility?
>>>>>>>>>
>>>>>>>>> Thank you.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>> Changwoon Jang,
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
>>>>>>>>> * Please search the archive at
>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>>> posting!
>>>>>>>>>
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>> || radhe radhe ||
>>>>>>>>
>>>>>>>> abhishek
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at
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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
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org
>>>>>>
>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> * Please search the archive at
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>>>> posting!
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>>
> --
> ==================================================
>
> 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
>
> * Please search the archive at
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