Re: [AMBER] PMEMD does not support intermolecular PRFs

From: Ross Walker <>
Date: Sun, 5 Jun 2011 22:12:55 -0700

Hi Maura,

The problem is NOT with your simulation protocol but with your underlying
prmtop. PMEMD does not support intermolecular PRF's (for NPT simulations)
because you should not be able to build a prmtop file with such a setup. So
the question is how EXACTLY did you build this prmtop file? - This is what
we need to debug since leap should not be building such prmtops.

A workaround for now is to run the NPT part in sander and then switch to NVT
with PMEMD once you have the density equilibrated. Although the correct
approach is to figure out how you are building such a system in the first

All the best

> -----Original Message-----
> From: Maura Catherine Mooney []
> Sent: Sunday, June 05, 2011 8:45 AM
> To:
> Subject: [AMBER] PMEMD does not support intermolecular PRFs
> 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 - 22:30:02 PDT
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