[gmx-users] About Box vector and solvation
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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