[gmx-users] constraints

[Justin Lemkul]

On 5/12/14, 6:14 AM, Nicola Staffolani wrote:
> Hi everybody,
> ​​
> I am running a simulation of a protein bonded on a metallic structure. In
> the mdp files of the MD run I have set
>
> constraints = none
>
> while during the equilibration I had set
>
> constraints = all-bond
>
> in order to reach the MD step with the structure of my protein still in
> order.
>
> Well, then I get the following message:
>
> WARNING 1 [file speptide.top, line 11134]:
>    The bond in molecule-type Protein_chain_B 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.
>
> ​But this is very strange because the bond between the aforementioned atoms
> is just copied from the Table 2.5.2.1 of the GROMOS Manual and User Guide.
> If then I set ​
>
>
> ​constraints = h-bonds
>
> then mdrun is running​, but I think it should run also with no constraints.
> Am I right? Any clue of what is going on? I have also noted that line 11134

If you set "constraints" to anything other than "none," there will be 
constraints applied as instructed.

> of speptide.top is jut the following (bold case) one, i.e. the last one of
> the file:
>
> ​[ molecules ]
> ; Compound        #mols
> Protein_chain_B     1
> SOL             14041
> *NA                  1​*
>

The line printed by the error message is largely irrelevant; it just tells you 
grompp has reached the end of the topology and has found an error.  Not very 
helpful in this case, but that's a separate issue.

If you remove constraints, you have to reduce your time step; that's what the 
warning is telling you.  The maximum time step allowed in the simulation is 
tightly coupled to what the intrinsic vibrational frequencies are.  See the 
Gromacs manual and LINCS or SHAKE papers if you are not familiar with this 
concept.  The warning tells you that there is an unconstrained bond between N-H 
that will oscillate too fast for your chosen time step.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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