[gmx-users] About Box vector and solvation

Justin Lemkul jalemkul at vt.edu
Mon Oct 29 15:06:02 CET 2012

On 10/29/12 9:59 AM, vidhya sankar wrote:
>   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)

There is nothing to do.  These steps corresponded to no change in energy.  It 
happens sometimes with EM.

> 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)

Never manually change a box vector.  Why would you do this?  Do you understand 
what InflateGRO is doing and why you shouldn't be making ad hoc changes?  Let 
the script do the work for you.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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