Okay, I don't know that much about the amoeba param issues here; that is
probably more of a Darden question. So from my perspective, the important
question is: what happens with sander? That is the "reference"
implementation, though I fixed several problems that existed in the
reference (relatively minor, if memory serves).
Regards - Bob Duke
----- Original Message -----
From: "Margaret Johnson" <mej47.berkeley.edu>
To: <amber.scripps.edu>
Sent: Tuesday, November 18, 2008 9:29 PM
Subject: AMBER: PMEMD with AMOEBA parms including a lone pair site
> Hi,
>
> I am trying to run pmemd using AMOEBA parameters (which I have previously
> done succesfully), where the DMSO molecule has an additional 'M' site
> defined at the lone pair position.
> While I have been able to generate the inpcrd and prmtop files using
> /amoeba_parm, /after one step in a pmemd NPT simulation, all the velocity
> dependent properties are NaN, while all the potential energy values are
> fine.
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = NaN PRESS =
> NaN
> Etot = NaN EKtot = NaN EPtot
> = -22940.5513
> BOND = 226.9192 ANGLE = 597.6138 DIHED
> = -226.2797
> 1-4 NB = 550.2788 1-4 EEL = 0.0000 VDWAALS =
> 1424.3225
> EELEC = -21829.1325 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = NaN VIRIAL = NaN VOLUME =
> 140608.0000
> EPOLZ = -3684.2734
> Dipole convergence: rms = 0.469E-04 iters = 14.00
> Density =
> 0.6981
>
> When I run the system using tinker programs, including /dynamic/, the
> system propagates succesfully. I have previously generated inpcrd and
> prmtop files with AMOEBA parameters (using /amoeba_parm) /for other
> systems that ran succesfully with pmemd, the only difference this time is
> the M site.
> This site has a mass of 1, and bond and angle constraints to maintain its
> position, but zero everything else, which are explicitly listed out. (vdw,
> torsions, multipoles, polarizability).
> I also tried restarting in pmemd using the /.dyn /output from a tinker
> dynamic run, which had the same problem as above.
> Is there some way to fix this? It doesn't seem like the M site is defined
> any differently than any other atoms, except for all the zeroed
> parameters.
>
> Thanks very much,
> Maggie Johnson
>
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Received on Fri Dec 05 2008 - 15:58:17 PST
