Hi Murat,
> This is MDin file:
> 1ns vacuum MD
> &cntrl
> imin = 0, ntb = 0,
> ntpr = 5000, ntwx = 1000, ntwr = 1000,
> ntt = 1, ntp = 0,
> tempi = 0.0, temp0 = 300.0,
> nstlim = 1000000,
> cut = 10.0
> &end
>
> and I get the following output message just at the instant of
> 0 ps of MD:
>
> Frac coord min, max: -3.26662690012118D-004 0.826317897389839
> [12] MPI Abort by user Aborting program !
> The system has extended beyond
> the extent of the virtual box.
Your system has blown up - before it has even reached 1000 steps and so no
mdcrd is written and no output info is given.
Try setting ntpr=1 and ntwx=1 and you will be able to watch it blowing up.
Note, you are doing a gas phase simulation here and you only have a cut off
of 10 A - both are not recommended. If you really must do gas phase then you
really want a cut off of at least 16 A or so... Ideally you should at least
attempt to do this in implicit solvent like GB or if you can do it in
explicit solvent with PME. You really can't expect a protein to be stable in
a vacuum. Try it in the lab. Take your protein in water solution and stick
it in a vacuum at 300K and watch it boil. Then see if you can ever condense
your protein back in an intact state.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Oct 26 2004 - 01:53:00 PDT
