[gmx-users] Grompp warning about topology constrains

[Justin Lemkul]

On 1/29/18 11:03 AM, Ahmed Mashaly wrote:
> Hi,
> I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization.
>
>
> For NVT, when I use grompp, this warning appears:
> WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an angle, connected by constraints and  with masses that differ by more than a factor of 13. This means that  there are likely dynamic modes that are only very weakly coupled. To  ensure good equipartitioning, you need to either not use constraints on  all bonds (but, if possible, only on bonds involving hydrogens) or use  integrator = sd or decrease one or more tolerances:  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=  4 or SHAKE tolerance <= 1e-05
>
> But in .top file there in this line (the last one) there is no such a thing.

The error appears at the end of topology parsing, so it reports the last 
line as being the source, but that's not correct. It's just a reflection 
of the fact that you're doing something unstable somewhere in the topology.

> It worked when I changed the integrator to sd or when I changed the constraints to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance <= 1e-05
>
>
> I even deleteddefine                  = -DPOSRES
> from the .mdp file and got the same warning

Position restraints have nothing to do with bond constraints.

The text below is basically unintelligible. Please use proper line 
wrapping in your email client.

-Justin

>
> this is my input file:itle                   = NVT define                  = -DPOSRES ; Run parametersintegrator              = md       dt                      = 0.002    nsteps                  = 250000   ; Output controlnstlog                  = 500     nstxout                 = 500    nstvout                 = 500     nstfout                 = 500     nstcalcenergy           = 10  nstenergy               = 500    ; Bond parameterscontinuation            = no       constraint_algorithm    = lincs       constraints             = all-bonds     lincs_iter              = 2           lincs_order             = 4          shake-tol = 1e-05  ; Neighborsearchingcutoff-scheme           = Verletns_type                 = grid           nstlist                 = 10            rlist                   = 1.0            rvdw                    = 1.0            vdwtype                 = Cut-offrcoulomb                = 1.0            ; Electrostaticscoulombtype             = pme            pme_order               = 4              fourierspacing          = 0.16
> ; Temperature couplingtcoupl                  = V-rescaletc_grps                 = Protein Non-Protein tau_t                   = 0.1    0.1ref_t                   = 300    300
> ; Pressure couplingpcoupl                  = no        ; Periodic boundary conditionspbc                     = xyz       ; Dispersion correctionDispCorr                = EnerPres  ;gen_vel                 = yes       gen_temp                = 300       gen_seed                = -1
>
>
>
> And these are the last lines of .top with line numbers (starting 79101)  79101 [ moleculetype ]  79102 ; Name            nrexcl  79103 SOL          3  79104   79105 [ atoms ]  79106 ;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB  79107 ; residue    1 WAT rtp WAT q 0.0  79108     1         OW      1    SOL     OW      1  -0.834000    16.0000   ; qtot -0.8340  79109     2         HW      1    SOL    HW1      2   0.417000     1.0080   ; qtot -0.4170  79110     3         HW      1    SOL    HW2      3   0.417000     1.0080   ; qtot 0.0000  79111   79112 #ifdef FLEXIBLE  79113   79114 [ bonds ]  79115 ;    ai     aj funct         c0         c1         c2         c3  79116       2      3     1   0.15136 462750.400000  79117       1      2     1   0.09572 462750.400000  79118       1      3     1   0.09572 462750.400000  79119   79120   79121 #else  79122   79123 [ settles ]  79124 ; i     funct   doh     dhh  79125 1     1   0.09572   0.15136  79126   79127 #endif  79128   79129 [ exclusions ]  79130 1  2  3  79131 2  1  3  79132 3  1  2  79133   79134 [ system ]  79135 ; Name  79136 Generic title  79137   79138 [ molecules ]  79139 ; Compound       #mols  79140 system1              1  79141 system2              1  79142 system1              1  79143 system2              1  79144 system1              1  79145 system2              1  79146 NA                   3  79147 SOL              49664
> Thanks,Ahmed

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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