> > PS: I was thinking to copy/paste the box info of the first inpcrd_01
> >
> > 38.6491104 38.6491104 38.6491104 109.4712190 109.4712190 109.4712190
> >
> > to the second inpcrd_02.
>
> This is worth a try (i.e. it should work, but test carefully!). Another
> option is use just the solute for the second case, and use trial and error
> with distance parameter in solvateoct to get the desired number of water
> molecules.
Dear Dave,
I have done 2 simulation, using the following combinations:
1. inpcrd_01 and prmtop_01
2. inpcrd_01 and prmtop_02
They gave exactly the same output files. After this simulation, I have
replaced the last line of inpcrd_02 with the last line of inpcrd_01. I
have used 'ambpdb' to create the corresponding .pdb files; namely 01.pdb
which is created using inpcrd_01/prmtop_01, and 02.pdb, which is created
using prmtop_02/inpcrd_02_mod (inpcrd_02_mod is the modified version of
inpcrd_02). I checked out both these .pdb files in VMD, and the rmsd value
is 0.0008.
My conclusion: Changing only the last line of the inpcrd_02 with the last
line of inpcrd_01 should solve this 'setbox' problem. I did not do any
long simulation, because if prmtop files are not responsible of this
problem (which is the case after doing the above 2 simulations), that
means that only changing the last line of inpcrd file, which stores the
cell box info in it, is responsible of this problem.
Thanks for your suggestions. Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Apr 02 2006 - 06:10:15 PDT
