Hi, Use a visualization program and see what you learn...
Mark On Mon, Aug 25, 2014 at 8:26 AM, Lovika Moudgil <lovikamoud...@gmail.com> wrote: > I am trying to have a system of GNPs with aminoacid and stabilizer i.e > Sodium Citrate ...and this hydrogen is of Sodium Citrate ..... moving > molecule is not working for me!!! > > Regards > Lovika > > > On Mon, Aug 25, 2014 at 10:52 AM, Kester Wong <kester2...@ibs.re.kr> > wrote: > > > If the H-atom is constituent of a molecule (e.g. H2O), then you could > also > > try moving the molecule coordinates and see how it goes. > > > > I had a similar issue, but moving the molecule by an angstrom worked in > my > > case. Good luck! > > > > > > > > Regards, > > > > Kester > > > > > > > > --------- 원본 메일 --------- > > > > *보낸사람* : Lovika Moudgil <lovikamoud...@gmail.com> > > *받는사람* : <gmx-us...@gromacs.org> > > *받은날짜* : 2014년 8월 25일(월) 13:52:49 > > *제목* : Re: [gmx-users] mdrun error > > > > Thanks for reply Justin and Kester...Ya my geometry is getting distorted > > and I tried to change the coordinates of atom 19 i.e Hydrogen ...but the > > error is same!!!! > > > > > > Regards > > Lovika > > > > > > On Mon, Aug 25, 2014 at 7:09 AM, Kester Wong wrote: > > > > > Dear Lovika, > > > > > > > > > Have you looked into atom 19 specifically? Perhaps, changing the > > > coordinate of atom 19 manually, and let it do another minimisation run > > > would solve the issue? > > > > > > > > > > > > Regards, > > > > > > Kester > > > > > > > > > --------- 원본 메일 --------- > > > > > > *보낸사람* : Lovika Moudgil > > > *받는사람* : > > > *받은날짜* : 2014년 8월 24일(일) 18:28:06 > > > *제목* : [gmx-users] mdrun error > > > > > > Hi everyone , > > > > > > Need some help .I have got an error in my mdrun . Upto grompp every > thing > > > was fine but when I give command for mdrun ,It stops with this ... > > > Steepest Descents: > > > Tolerance (Fmax) = 1.00000e+03 > > > Number of steps = 10000 > > > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.08534e+18 Fmax= inf, > atom= 19 > > > Energy minimization has stopped, but the forces have not converged to > the > > > requested precision Fmax < 1000 (which may not be possible for your > system). > > > It stopped because the algorithm tried to make a new step whose size > was too > > > small, or there was no change in the energy since last step. Either > way, we > > > regard the minimization as converged to within the available machine > > > precision, given your starting configuration and EM parameters. > > > > > > Double precision normally gives you higher accuracy, but this is often > not > > > needed for preparing to run molecular dynamics. > > > 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 = 2.0853354e+18 > > > Maximum force = inf on atom 19 > > > Norm of force = 1.7429674e+18 > > > > > > constraints are all ready none ...Please help me what should I do to > solve > > > this . > > > Thanks and Regards > > > Lovika > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > > > * Can't post? 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