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 <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