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

[Mark Abraham]

On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri <francesco.oteri at gmail.com
> wrote:

> 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.
>

I highly doubt the different sizes are relevant. They're just changing the
starting position enough to make a numerical difference.

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!
>

Yeah, and since all your stages work in theory, you don't have a problem
:lol:

There's a reason the link I gave has "visualise" as the first diagnostic
suggestion. Your eyes are much better at seeing problems than your brain is
at writing bulletproof scripts.

Mark


>
> 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)
> >> Starting 12 tMPI threads
> >> Using 12 MPI threads
> >> 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>
> >
> > ==============================**==========
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>