[gmx-users] constraints

Mon May 12 15:03:18 CEST 2014

Hi Justin,

thank you for your clear reply!

However, it still comes as surprising to me that a "standard" N-H bond
(entered as a gb_2 one with the same parameters as described in Table
2.5.2.1 of the GROMOS96 Manual and User Guide) enters in conflict with the
standard dt value: indeed dt = 0.002 → tau < 5 · dt and dt = 0.001 → tau <
10 · dt (where with tau I have meant the period associated to the harmonic
frequency) but dt = 0.001 is right the default
value<http://manual.gromacs.org/online/mdp_opt.html#pp>of dt! So it's
like who constructed GROMACS didn't know that using the
default dt value and by just bonding a H atom to a N one would produce a
WARNING...  What am I missing?

By the way, I have done an estimate of tau = 2 · pi · sqrt(µ/k), where µ =
m_H · m_N / (m_H + m_N) is the reduced mass of H and N and it looks right
what the WARNING is asserting...

On Mon, May 12, 2014 at 2:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36