[gmx-users] About Usage of Constraints

[Justin Lemkul]

On 10/7/12 12:24 AM, vidhya sankar wrote:
> Dear justin Thank you for your previous reply
>                                                                          I  am running NPT Equlibration  at 20 ps  with dt 0.0002 in 100000 steps  Without usage of  Lincs Algorithm and its related parameters it runs Successfully .
> But When I  Increase dt from 0.0002 to 0.002 then I have got error as follows in grompp
>
> WARNING 1 [file 2KDQTR.top, line 71]:
>    The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
>    an estimated oscillational period of 1.0e-02 ps, which is less than 5
>    times the time step of 2.0e-03 ps.
>    Maybe you forgot to change the constraints mdp option.
>

One cannot arbitrarily increase the timestep to such a value without using 
constraints.  The relationship between timestep and bond vibrational frequencies 
is discussed in every major simulation textbook.

> Then I have used the Lincs Algorithm and its related parameter Then I have got Error during Mdrun as follows I  saw  there Are Plenty Of discussion in Mailing list   But  I am Not Able to come to conclusion
>
>
> relative constraint deviation after LINCS:
> rms 0.015272, max 0.577865 (between atoms 120 and 122)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
> Wrote pdb files with previous and current coordinates
>
>     129    131   39.1    0.1475   0.1664      0.1330
>      129    130   37.8    0.1191   0.1243      0.1230
>      125    126   38.5    0.1738   0.1508      0.1530
>      124    129  103.2    0.0962   0.9157      0.1530
>      124    125  124.3    0.1725   0.8648      0.1530
>      122    124  169.9    0.4717   2.5621      0.1470
>      122    123  168.0    0.2655   3.1890      0.1000
>      120    122  176.3    0.5957   7.3414      0.1330
>      120    121  172.8    0.5550   6.4843      0.1230
> What does the Above Fact Indicates I mean the Problem is in Topology or in MD Parameter file ?
>

Either, or both.  It's impossible to say without a more thorough description of 
your system, what you have done to minimize and equilibrate it, and what you're 
trying to do.  Basically everything you would be advised is already described here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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