[gmx-users] constraint

Thu Dec 15 21:53:14 CET 2016

Hi,

Like the warning says, you need a smaller time step or bond constraints.
I'm sure that whoever designed this model had one of those in mind and you
are closely consulting what they wrote :-)

Mark

On Thu, 15 Dec 2016 23:20 NIKHIL JOSHI <nikhil.joshi926 at gmail.com> wrote:

> GMX Users:
>
> When I run grompp on Polyetylene Oxide in water, I get the following Note:
>
> NOTE 2 [file topol-trappeR-B.top, line 423]:
>   The bond in molecule-type PEO between atoms 2 O12 and 3 C23 has an
>   estimated oscillational period of 6.0e-03 ps, which is less than 10 times
>   the time step of 1.0e-03 ps.
>   Maybe you forgot to change the constraints mdp option.
>
> Here is my mdp file
>
> ; RUN CONTROL PARAMETERS
> integrator               = md
>
> ; Start time and timestep in ps
> dt                       = 0.002  ; 2 fs
> nsteps                   = 250000 ; 5 ns
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout                  = 0 ;
> nstvout                  = 0 ;
> nstlog                   = 500   ; 1ps
> nstenergy                = 500 ; 1 ps
> nstxtcout                = 500 ; 1ps
> xtc-precision            = 1000
> xtc-grps                 = System
>
> ; ENERGY EXCLUSION
> energygrps = System
> ;comm_mode = none
> ;nstcomm = 1000000
>
> ; BOUNDARY CONDITIONS
> pbc                      = xyz
>
> ; NEIGHBOR SEARCHING PARAMETERS
> cutoff-scheme     = Verlet
> nstlist                  = 40
> ns_type                  = grid
> rlist                    = 1.0
>
> ; Method for doing Van der Waals
> vdwtype                  = Cut-off
> rvdw                     = 1.0
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> rcoulomb                 = 1.0
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
>
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
>
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl                   = nose-hoover
> tc-grps                  = System
> tau_t                    = 2.5
> ref_t                    = 300
> ; Pressure coupling
> ;Pcoupl                   = Parrinello-Rahman
> ;Pcoupltype               = Isotropic
> ;tau_p                    = 5.0
> ;ref_p                    = 1.0
> ;compressibility          = 4.5e-05
>
> ; OPTIONS FOR BONDS
> constraints              = h-bonds
> constraint_algorithm     = SHAKE
> ; Relative tolerance of shake
> ;shake-tol                = 1e-04
>
> Here is my top file:
> ; SINGLE CHAIN PEO [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ
> fudgeQQ 1 2 no [ atomtypes ] ; name at.num mass charge ptype sigma epsilon
> (TRAPPE MODEL) OW 15.99940 -0.8476 A 3.16557e-01 6.50194e-01 HW 1.00800
> 0.4238 A 0.00000e+00 0.00000e+00 C2 14.02700 +0.250 A 3.95000e-01
> 3.82467e-01 C3 15.03500 +0.250 A 3.75000e-01 8.14821e-01 O1 15.99940 -0.500
> A 2.80000e-01 4.57000e-01 [ bondtypes ] ;i j func b0 kb OW HW 1 0.100
> 345000 HW HW 1 0.16330 345000 C2 C2 1 0.15400 376000 C3 O1 1 0.14100 267900
> C2 O1 1 0.14100 267900 [ angletypes ] ;i j k func th0 cth C2 O1 C2 1 112
> 519.6 C3 C2 O1 1 112 418.2 [ dihedraltypes ] ;i j k l func c0 c1 c2 c3 c4
> c5 (kJ/mol) C3 O1 C2 C2 3 -5.1599 -0.6971 5.35013 0.80312 0.28307 0.09526
> O1 C2 C2 O1 3 7.58526 6.70523 8.40071 0.63221 0.11063 0.35962 C2 C2 O1 C3 3
> -5.1599 -0.6971 5.35013 0.80312 0.28307 0.09526 [ moleculetype ] PEO 3 [
> atoms ] ; nr type resnr residue atom cgnr charge 1 C3 1 PEO C31 1 0 2 O1 1
> PEO O12 1 0 3 C2 1 PEO C23 1 0 4 C2 1 PEO C24 2 0 5 O1 1 PEO O15 2 0 6 C2 1
> PEO C26 2 0 7 C2 1 PEO C27 3 0 8 O1 1 PEO O18 3 0 9 C2 1 PEO C29 3 0 10 C2
> 1 PEO C210 4 0 11 O1 1 PEO O111 4 0 12 C2 1 PEO C212 4 0 13 C2 1 PEO C213 5
> 0 14 O1 1 PEO O114 5 0 15 C3 1 PEO C315 6 0 [ bonds ] ;i j funct length
> force.c 1 2 1 0.141 8180000 2 3 1 0.141 8180000 3 4 1 0.154 7150000 4 5 1
> 0.141 8180000 5 6 1 0.141 8180000 6 7 1 0.154 7150000 7 8 1 0.141 8180000 8
> 9 1 0.141 8180000 9 10 1 0.154 7150000 10 11 1 0.141 8180000 [ angles ] ; i
> j k funct theta force.c 1 2 3 1 112 519.6 2 3 4 1 112 418.2 3 4 5 1 112
> 418.2 4 5 6 1 112 519.6 5 6 7 1 112 418.2 6 7 8 1 112 418.2 7 8 9 1 112
> 519.6 8 9 10 1 112 418.2 9 10 11 1 112 418.2 10 11 12 1 112 519.6 [
> dihedrals ] ;i j k l func c0 c1 c2 c3 c4 c5 1 2 3 4 3 -5.15997 -0.69711
> 5.35013 0.80312 0.28307 0.09526 2 3 4 5 3 7.58526 6.70523 8.40071 0.63221
> 0.11063 0.35962 3 4 5 6 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526
> 4 5 6 7 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526 5 6 7 8 3
> 7.58526 6.70523 8.40071 0.63221 0.11063 0.35962 6 7 8 9 3 -5.15997 -0.69711
> 5.35013 0.80312 0.28307 0.09526 7 8 9 10 3 -5.15997 -0.69711 5.35013
> 0.80312 0.28307 0.09526 8 9 10 11 3 7.58526 6.70523 8.40071 0.63221 0.11063
> 0.35962 9 10 11 12 3 -5.15997 -0.69711 5.35013 0.80312 0.28307 0.09526 [
> moleculetype ] ;molname nrexcl SOL 2 [ atoms ] ; nr type resnr residue atom
> cgnr charge mass 1 OW 1 SOL OW 1 -0.8476 2 HW 1 SOL HW1 1 0.4238 3 HW 1 SOL
> HW2 1 0.4238 [ bonds ] ; i j funct length force.c. 1 2 1 0.10000 345000 1 3
> 1 0.10000 345000 2 3 1 0.16330 345000 [ system ] PEO-SINGLECHAIN [
> molecules ] PEO 1
>
> Do I need to add some sort of constraint on my methanol molecule?
>
> Thanks,
> Nik
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