I have a simulation of 4 oligomers in a box of water. What puzzles me is, when I looked at the pdb file of the restart file (min1.pdb), it shows all 4 of the oligomers within the box of water. But when I looked at the first trajectory produced (eq1a.pdb), it shows that some part of the oligomers are outside the water box. Can someone tell me what I did wrong?
I made sure the input coordinate of the MD run to be the restrt file of the minimization run. Here is the snippet from the MD run:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 12/11/2012 at 16:15:00
File Assignments:
| MDIN: eq1a.inp
| MDOUT: mdout.eq1a
| INPCRD: restrt.min1a
| PARM: oligo-water.prmtop
| RESTRT: restrt.eq1a
| REFC: refc
The INPCRD is shown to be the correct file, but I don't get how the structure of the first run is different.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
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Received on Tue Dec 11 2012 - 15:00:02 PST
