On Wed, May 1, 2013 at 3:16 PM, 라지브간디 <[email protected]> wrote:
> Dear > Mark, > > > > > As per you suggestion, I have simulated a single CO as well as > CO-with-vsite in a box. > > > > > A single CO runs without any problem, BUT the CO-with-vsite > gives an same error as before: > > > > > Steepest > Descents: > > Tolerance (Fmax) = > 1.00000e+03 > > Number of steps = > 50000 > > Step= 0, Dmax= 1.0e-02 nm, Epot= > -3.73341e+04 Fmax= 3.38911e+05, atom= 2 > > Step= 1, Dmax= 1.0e-02 nm, Epot= > -4.54970e+04 Fmax= 4.95889e+05, atom= 2 > > Step= 2, Dmax= 1.2e-02 nm, Epot= > -6.18180e+04 Fmax= 9.34585e+05, atom= 2 > > Step= 3, Dmax= 1.4e-02 nm, Epot= > -1.10395e+05 Fmax= 3.03088e+06, atom= 1 > > Step= 5, Dmax= 8.6e-03 nm, Epot= > -2.09874e+05 Fmax= 1.09138e+07, atom= 2 > > Step= 9, Dmax= 1.3e-03 nm, Epot= > -2.42526e+05 Fmax= 1.45550e+07, atom= 1 > > Step= 11, Dmax= 7.8e-04 nm, Epot= > -2.67493e+05 Fmax= 1.76910e+07, atom= 2 > > Step= 14, Dmax= 2.3e-04 nm, Epot= > -2.76005e+05 Fmax= 1.88299e+07, atom= 2 > > Step= 16, Dmax= 1.4e-04 nm, Epot= > -2.81365e+05 Fmax= 1.95651e+07, atom= 2 > > Step= 19, Dmax= 4.2e-05 nm, Epot= > -2.83032e+05 Fmax= 1.97967e+07, atom= 1 > > Step= 23, Dmax= 6.3e-06 nm, Epot= > -2.83281e+05 Fmax= 1.98315e+07, atom= 1 > > Step= 26, Dmax= 1.9e-06 nm, Epot= > -2.83355e+05 Fmax= 1.98418e+07, atom= 2 > > Step= 28, Dmax= 1.1e-06 nm, Epot= > nan Fmax= 0.00000e+00, atom= 0 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > > Double precision normally gives you higher > accuracy. > > > > > writing lowest energy coordinates. > > > > > Back Off! I just backed up min.gro to ./#min.gro.1# > > > > > Steepest Descents converged to machine precision in > 29 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -2.8335531e+05 > > Maximum force = 1.9841798e+07 > on atom 2 > > Norm of force = 1.6200760e+07 > > > > > > > > I am afraid that I am a making any mistakes of setting the > vsite? > > > > > > My > topology file vsite setting : > > > > > [ moleculetype ] > > > ; > Name nrexcl > > Other_chain_A 3 > > > > [ atoms ] > > ; nr type resnr > residue atom cgnr charge mass > typeB chargeB massB > > ; residue 157 CMO rtp CMO q -1.6 > > 1 > C 157 CMO C > 1 -0.75 12.011 ; qtot -0.75 > > 2 > O 157 CMO O > 2 -0.85 15.9994 ; qtot -1.6 > > 3 > I 157 CMO I > 3 1.6 0.0000 > > [ bonds ] > > ; ai aj funct > c0 c1 > c2 > c3 > > 1 2 2 > gb_4 > > [ virtual_sites2 ] > > ; Vsite from funct > a > > > > > 3 1 2 > 1 0.4376625 > > > > > > > > My coordiante (.gro) file where i added the vsite xyz: Also included > the vsite atom info in atomypes as well as ffnonbonded.itp. > > > > > Gravel > Rubs Often Many Awfully Cauterized Sores > > > 3 > > > 157CMO C 1 1.625 2.697 > 0.490 > > > 157CMO O 2 1.722 2.647 > 0.482 > > > 157CMO I 3 1.673 2.672 > 0.486 > > 0.09660 > 0.05040 0.00760 > > This box is far too small. Mark > ~ > > > > > > > Could you tell what mistakes I am making here ? > > > > > > Thanks in advance. > > > > > > Raju > > > > > > On Wed, May 1, 2013 at ��������������� : > > > > I mean simulate a single CO in a box. Then CO-with-vsite in a box. > If you > can do that, then a bunch of problems are known to be solved. Leaping in > the deep end with a complex system means you don't know where the trouble > comes from when you have it. > > Mark > > On Wed, May 1, 2013 at 8:45 AM, ��������������� > <[email protected]> wrote: > > > Dear Mark, > > > > > You mean do the CO simulation and then add V-site upon > production run? > > > > Could you please more specific, what has to be done to avoid this > error? > > > > > > > On Fri, Apr 26, 2013 at 6:16 PM, ������������������������������ > <[email protected]> wrote: > > > > Maybe your starting configuration of atoms is too broken to be > useful. > > Maybe you have some interaction on atom 2513 that doesn't work. > > > > Make a simple system of CO work, then do CO+vsite. Then apply those > lessons > > to your complex system. > > > > Mark > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
