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

========================================
--
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

Reply via email to