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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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