[gmx-users] Grompp warning about topology constrains
Justin Lemkul
jalemkul at vt.edu
Tue Jan 30 18:00:21 CET 2018
On 1/30/18 5:46 AM, Ahmed Mashaly wrote:
>
> Thanks Justin ... The topology seems fine to me
>
> The inputs are in this link incase of the text is messed again
> https://drive.google.com/open?id=13DzlUl0rLoJBfr_oPf9tLPknAsRNJpuR
>
>
>
> title = NVT
> define = -DPOSRES ;
>
> ; Run parameters
> integrator = md
> dt = 0.002
> nsteps = 250000
>
> ; Output control
> nstlog = 500
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstcalcenergy = 10
> nstenergy = 500
>
> ; Bond parameters
> continuation = no
> constraint_algorithm = lincs
> constraints = all-bonds
> lincs_iter = 2
> lincs_order = 4
> shake-tol = 1e-05
>
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid
> nstlist = 10
> rlist = 1.0
> rvdw = 1.0
> vdwtype = Cut-off
> rcoulomb = 1.0
>
> ; Electrostatics
> coulombtype = pme
> pme_order = 4
> fourierspacing = 0.16
>
> ; Temperature coupling
> tcoupl = V-rescale
> tc_grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
>
> ; Pressure coupling
> pcoupl = no
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr = EnerPres
>
> ;
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
>
>
>
>
>
> The last lines of toplogy:
As I said before, the line numbers here and their contents are irrelevant.
The error message and its solution are quite clear. You have at least
one angle between some atoms i-j-k, in which the masses of atoms i and k
differ by at least a factor of 13. In this instance, you shouldn't be
constraining all bonds. Set constraints = h-bonds and move ahead. The
only force field that I know of that requires all bonds to be
constrained is GROMOS, all others normally only constrain bonds to H.
-Justin
> 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
>
>
>
>
>
> Kind Regards,
> Ahmed
>
>
>
>
>
> ________________________________
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Sent: Tuesday, January 30, 2018 2:14 AM
> Subject: Re: [gmx-users] Grompp warning about topology constrains
>
>
>
>
>
> 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 0.0957
> 2 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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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