# [gmx-users] Error with MARTINI depending by the box size

francesco oteri francesco.oteri at gmail.com
Mon Dec 10 23:15:43 CET 2012

```Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.

I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid the error is 19.5nm.
My system has an average size and, as stated by vmd, it size are
X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986
So a box of 20nm, as well as 19nm, is large enough to accomodate the
protein.

Moreover, since I remove the water around the protein (that is already
stabie because of the in vacuo minimization), the problem has to be in the
bulk water!

Francesco

2012/12/10 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 12/10/12 3:48 PM, francesco oteri wrote:
>
>> Dear gromacs users,
>>
>> I am facing a very tricky problem in building a stable topology.
>> In particular I am trying to use MARTINI force-field and I noticed that if
>> I use a box whose the side size is smaller than 20nm, the minimization
>> fails with this message:
>>
>> Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
>> Making 2D domain decomposition 4 x 3 x 1
>>
>> Steepest Descents:
>> Tolerance (Fmax) = 1.00000e+03
>> Number of steps = 2000
>> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
>> Energy minimization has stopped, but the forces havenot converged to the
>> requested precision Fmax < 1000 (whichmay not be possible for your
>> system).
>> It stoppedbecause the algorithm tried to make a new step whose sizewas too
>> small, or there was no change in the energy sincelast step. Either way, we
>> regard the minimization asconverged to within the available machine
>> precision,given your starting configuration and EM parameters.
>>
>> Double precision normally gives you higher accuracy, butthis is often not
>> needed for preparing to run moleculardynamics.
>> You might need to increase your constraint accuracy, or turn
>> off constraints altogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy = 4.4209897e+18
>> Maximum force = inf on atom 39063
>> Norm of force = inf
>>
>>
> With this information, you should be able to deduce the source of the
> problem.
>
>
>  gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
>>
>> But, if I use a box bigger then 19.5nm the minimization, although with
>> some
>> LINCS warning, succeeded!
>>
>>
> These LINCS warnings will also give the same information as to where
> problems start.
>
>
>  I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.
>>
>> I am attaching the script (crea_topo.csh) I am using to build the
>> topologies as well as all the input files you need to replicate the error.
>>
>> The different topologies have been obtained changing the value of the
>> variable side in crea_topo.csh
>>
>>
> How many values you have tried?  What is the minimum box size necessary to
> accommodate your system?  This all seems like random failures from unstable
> configurations.
>
>
>  As you can notice from the script, the structure is initially minimized in
>> vacuo to remove problems due in the all atoms-coarse grained
>> transformation
>> and then it is solvated, Then, water molecules closer then 0.8nm to
>> protein
>> are rmoved through vmd.
>>
>>
> What was the outcome of the in vacuo minimization?
>
>
>  Can you give me some clue on how to solve the problem, except changing the
>> software?.
>>
>>
> http://www.gromacs.org/**Documentation/Terminology/**
> Blowing_Up#Diagnosing_an_**Unstable_System<http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System>
>
> -Justin
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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--
Cordiali saluti, Dr.Oteri Francesco

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