Dear Amber Users,
Attached are the input files for lambda=0.50 for step2w (vdW softcore with no charge solute by scmask).
You can easily run the simulation by yourself.
The command to run these simulations is, for example,
mpirun -np 2 sander.MPI -O -ng 2 -groupfile group_min_l0.50
mpirun -np 8 sander.MPI -O -ng 2 -groupfile group_equil_l0.50
mpirun -np 8 sander.MPI -O -ng 2 -groupfile group_prod_l0.50
It will take some hours by 8 cpu cores, but if you decrease the total timestep to 0.1 ns or something,
it will finish soon.
(note that no constraint simulations also showed the nonzero DV/DL ELEC)
If you find something wrong, please let me know.
or is this a bug perhaps?
I have also the very related question.
We had the following output as already shown.
DV/DL, AVERAGES OVER 2500000 STEPS
NSTEP = 2500000 TIME(PS) = 6000.000 TEMP(K) = 7.64 PRESS = 0.0
Etot = 23.4943 EKtot = 23.4943 EPtot = 7.8078
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -6.9264
EELEC = 0.5888 EHBOND = 0.0000 RESTRAINT = 14.1454
EAMBER (non-restraint) = -6.3376
DV/DL = 7.8078
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 1.4092
Density = 0.0229
Ewald error estimate: 0.6058E-07
------------------------------------------------------------------------------
What is the above RESTRAINT term? This value is very different from the RESTRAINT value
written after "A V E R A G ES O V E R 2500000 S T E P S", and the above RESTRAINT value after
" DV/DL, AVERAGES OVER 2500000 STEPS" had very large values especially for small lambda (decoupling).
Hiro
> > But the output file from step2w/ included ELEC term for DV/DL.
> >
> > EELEC = 0.5888 EHBOND = 0.0000 RESTRAINT =
> 14.1454
>
> It would be very helpful to have the actual input files for a short run that
> illustrates the above behavior. You describe a procedure to create such
> files, but some parts of the description are a little vague, and even in the
> best circumstances it would take quite a lot of work to get to a working test
> case.
>
> ...thx...dac
>
>
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Received on Thu Oct 04 2012 - 20:30:03 PDT
