[gmx-users] About Box vector and solvation

vidhya sankar scvsankar_agr at yahoo.com
Mon Oct 29 14:59:58 CET 2012

 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)   

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