Hi all,
Perhaps someone could provide some advice on the following issue. I've only come across one instance of this on the mailing list and, as far as I can see, the issue wasn't resolved. I'll try to briefly explain. I'm running some MD simulations. The protocol I'm intending to run is basically,5000steps solvent restrained minimization,7500steps full system minimization, 50ps heating MD (classical), 1ns classical equilibration MD, then switch to qmmm MD for 1ns equilibration and finally 10ns qmmm production... (equil and prod will be run longer, if necessary). Using the pmemd module of amber the mini1, mini2 and cmd1 are successful, but the cmd2 fails with error 'PMEMD does not support intermolecular PRFs'. The issue I read previously on the mailing list mentioned input problems, but would the problem not arise in either the mini1, mini2 or cmd1 before this? An interesting point to note is the fact that this cmd2 job runs using sander. Both pmemd and sander use the same input files (*.prmtop, *.in and *.
inpcrd/*.rst). Also, both sander and pmemd are run using the *.MPI version.
Here is the input file for the cmd2 job:
#title
&cntrl
imin=0, irest=1, ntx=5,
ntb=2, ntp=1,
taup=2.0,
cut =12.0,
ntc=2, ntf=2,
tempi=300.0, temp0=300.00,
ntt=3, gamma_ln=2.0,
nstlim=500000, dt =0.001,
ntpr=5000, ntwx=5000, ntwr=5000,
/
Is the protocol and input file reasonable? Why does the pmemd job, but not the sander job fail? If the pmemd job fails, how reliable is the sander job? Could anyone provide any advice on the pmemd issue, as 1) my other simulations are run using pmemd, and 2) of, course, we see the large speed up!
Thanking you in advance.
Maura
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Received on Sun Jun 05 2011 - 09:00:03 PDT
