# Nvt.mdp unknown warning(Lincs warning)

**URL:** <https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119>\
**Category:** User discussions\
**Created:** [November 19, 2020, 3:06am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119 "2020-11-19T03:06:43Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![Fereshteh](https://avatars.discourse-cdn.com/v4/letter/f/b3f665/32.png) [@Fereshteh](https://gromacs.bioexcel.eu/u/Fereshteh)\
**Post date:** [November 19, 2020, 3:06am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/1 "2020-11-19T03:06:43Z")

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GROMACS version:2018

Hi dear users,  
I want to perform MD simulation on a protein containing 3 Zn ions by amber99sb force field.by -his and CYM and applying distance restraint, zn ions fixed in their position with out any movement but after energy minimization I got the bellow warnings,now I do not know how to change nvtmdp parameters number to solve the problem.

''WARNING 1 [file topol.top, line 86896]:  
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

Number of degrees of freedom in T-Coupling group Protein\_ZN is 18332.72  
Number of degrees of freedom in T-Coupling group NA\_CL\_Water is 177762.28  
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K  
Calculated rlist for 1x1 atom pair-list as 0.935 nm, buffer size 0.035 nm  
Set rlist, assuming 4x4 atom pair-list, to 0.900 nm, buffer size 0.000 nm  
Note that mdrun will redetermine rlist based on the actual pair-list setup  
Calculating fourier grid dimensions for X Y Z  
Using a fourier grid of 64x72x60, spacing 0.151 0.155 0.158  
Estimate for the relative computational load of the PME mesh part: 0.19  
This run will generate roughly 8 Mb of data’’

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 19, 2020, 9:36am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/2 "2020-11-19T09:36:53Z")

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Hi,  
how did you restraint the ZN distance?  
I sugget to restrain using an harmonic potential (func 6 in table [http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table](http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table)).  
Previously for Zn-N(HIS) I have use this setting : 0.207 for b0 and 4000 for k0 together with funct 6, and it works well

Best regards  
Alessandra

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<div class="post-metadata">

**Author:** ![Fereshteh](https://avatars.discourse-cdn.com/v4/letter/f/b3f665/32.png) [@Fereshteh](https://gromacs.bioexcel.eu/u/Fereshteh)\
**Post date:** [November 19, 2020, 4:30pm UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/3 "2020-11-19T16:30:29Z")

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Hi Dear Alevilla,  
Thanks for your respose.and for cystein what should I do? and my distance restraint is:  
distance\_restraints ]  
; ai aj type index type’ low up1 up2 fac  
9215 745 1 0 1 0.0 0.3 0.4 1.0  
9215 800 1 0 1 0.0 0.3 0.4 1.0  
9215 1054 1 0 1 0.0 0.3 0.4 1.0  
9215 1098 1 0 1 0.0 0.3 0.4 1.0  
9216 218 1 1 1 0.0 0.3 0.4 1.0  
9216 245 1 1 1 0.0 0.3 0.4 1.0  
9216 477 1 1 1 0.0 0.3 0.4 1.0  
9216 561 1 1 1 0.0 0.3 0.4 1.0  
9217 53 1 2 1 0.0 0.3 0.4 1.0  
9217 98 1 2 1 0.0 0.3 0.4 1.0  
9217 375 1 2 1 0.0 0.3 0.4 1.0

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 20, 2020, 10:28am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/4 "2020-11-20T10:28:32Z")

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Hi,  
the distance restraints you are using are developed to account for NMR data. If you want to use them, I suggest to tune the values for your specific case.  
See here more details on distance restraint

> **[Restraints — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/reference-manual/functions/restraints.html?highlight=distance)**

I suggest to use simple distance restraints (option 1 in the manual). For Zn distance you can take for example an values of the Zn-X that is observed experimentally.

Best regards  
Alessandra

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<div class="post-metadata">

**Author:** ![Fereshteh](https://avatars.discourse-cdn.com/v4/letter/f/b3f665/32.png) [@Fereshteh](https://gromacs.bioexcel.eu/u/Fereshteh)\
**Post date:** [November 21, 2020, 7:23pm UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/5 "2020-11-21T19:23:01Z")

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Hi,  
I tried harmonic potential too and also change my distance restraint but again faced with those warnings that I was mentioned in my post.as my em.gro is ok can I continue with maxwarn? I do not understand where is the problem!

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 23, 2020, 9:32am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/6 "2020-11-23T09:32:52Z")

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Hi,  
I see. The warning is not connected with the Zn, but to the use of constraints. With AMBER force field use constraint only the h-bonds, to be in line with the force field parameterization.

best regards  
Alessandra

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<div class="post-metadata">

**Author:** ![Fereshteh](https://avatars.discourse-cdn.com/v4/letter/f/b3f665/32.png) [@Fereshteh](https://gromacs.bioexcel.eu/u/Fereshteh)\
**Post date:** [November 23, 2020, 12:02pm UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/7 "2020-11-23T12:02:10Z")

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I try It even with out distance\_restraint,but again I was faced with this warnings

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<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 23, 2020, 12:39pm UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/8 "2020-11-23T12:39:44Z")

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Hi,  
What I meant that the warning is not related to distance restraint, but to the `constraints` definition, that you use in mdp file. My guess is that you use all-bonds, but the warning suggests to use h-bonds (as option).

See [http://manual.gromacs.org/current/user-guide/mdp-options.html#bonds](http://manual.gromacs.org/current/user-guide/mdp-options.html#bonds)

Best regards  
Alessandra

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<div class="post-metadata">

**Author:** ![Fereshteh](https://avatars.discourse-cdn.com/v4/letter/f/b3f665/32.png) [@Fereshteh](https://gromacs.bioexcel.eu/u/Fereshteh)\
**Post date:** [December 1, 2020, 4:52am UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/9 "2020-12-01T04:52:46Z")

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Hi,  
my problem was solved by harmonic potential.now for calculating RMSD I get this error:  
WARNING: Masses and atomic (Van der Waals) radii will be guessed  
based on residue and atom names, since they could not be  
definitively assigned from the information in your input  
files. These guessed numbers might deviate from the mass  
and radius of the atom type. Please check the output  
files if necessary.

Can not find mass in database for atom ZN in residue 702 ZN  
Can not find mass in database for atom ZN in residue 703 ZN  
Can not find mass in database for atom ZN in residue 704 ZN

I added zn atoms in index now I do not know which part of my index has a problem?

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [December 1, 2020, 6:12pm UTC](https://gromacs.bioexcel.eu/t/nvt-mdp-unknown-warning-lincs-warning/1119/10 "2020-12-01T18:12:12Z")

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The database is case-sensitive. Change ZN to Zn and it should match the element entry.