On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri <francesco.ot...@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 <jalem...@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@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-requ...@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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists