Dear Justin Thank you For you Previous reply. When I use inflate script There is Automatic Change in the box Vector At the End line of .gro file (output of inflate script) Then I have Done EM without Changing the Box Vector in the output of inflate script. in the screen i Have Observed the Following Discrepancy As follows .
Step= 2, Dmax= 1.2e-02 nm, Epot= -7.91260e+04 Fmax= 2.30915e+03, atom= 6104 Step= 4, Dmax= 7.2e-03 nm, Epot= -7.93164e+04 Fmax= 7.83650e+03, atom= 85 Step= 7, Dmax= 1.2e-02 nm, Epot= -8.08972e+04 Fmax= 7.87323e+03, atom= 85 Step= 9, Dmax= 7.5e-03 nm, Epot= -8.11951e+04 Fmax= 3.15522e+03, atom= 85 It quits Step 3 ,4 and step 8 ( When i open em.log files Energy Corresponding to 3 and 4 As follows) Step Time Lambda Step Time Lambda Step Time Lambda 8 8.00000 0.00000 3 3.00000 0.00000 4 4.00000 0.00000 What it shows ? How to rectify this Problem ( I have used .mdp file in your Website) Can i change the box Vector in .gro file of EM output ( I cannot change Box vector in System_inflated .gro As you Told me) -- 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
