Hai,.
Currently I am doing TI calculations on my receptor molecule(with periodic
box,and with water molecules). After a long simulations of 40ns, one of the
water molecule has drifted so far, that the rst file got corrupted i.e. I am
getting ***** instead of the coordinates. Then I ran sander simulations
with the previous uncorrupted file by making ntx=1, tempi =0 for 20ps to
get new rst files. By taking this I ran the simulation for 2ns but again the
rst file got corrupted due to the same reason.
So I have decided to generate new .rst file using ptraj
trajin recp.rst
center :1-1541
image familiar
trajout recp_new.rst restart
The new rst was created with zero velocities, and I have taken the
velocities from the last uncorrupted rst file into the new rst file. But
now when I am trying to run the simulation it is stopping at the following
point
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 61091
| TOTAL SIZE OF NONBOND LIST = 952727
I have cross checked the previous rst files with the new one. The alignment
and no of lines are same, but they are differing in the number of characters
by 60. I am unable to sort out what to do next. Please give me some
suggestion.
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Wed May 12 2010 - 15:00:03 PDT
