[gmx-users] constraint

NIKHIL JOSHI nikhil.joshi926 at gmail.com
Fri Dec 16 05:32:39 CET 2016 

Thank you sir for your reply. Methanol is my next phase of my project. I
forget to remove the final line.



On Fri, Dec 16, 2016 at 2:23 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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