Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask

From: <hironori.kokubo.takeda.com>
Date: Fri, 5 Oct 2012 12:27:07 +0900

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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Thu Oct 04 2012 - 20:30:03 PDT
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