Hi Marek,
Thanks for reporting this - can you try this again with pmemd.cuda_DPFP please and see if you see the same behavior.
All the best
Ross
> On Feb 9, 2017, at 10:09, Marek Maly <marek.maly.ujep.cz> wrote:
>
> Hello,
>
> I tried to minimize small molecule in vacuum condition with pmemd.cuda
> [Amber 16, actualized].
>
> Here is the content of the mdin file:
>
> ----------------
> &cntrl
> imin=1,maxcyc=5000,ncyc=4900,
> ntb=0,
> igb=6,cut=9999.0,
> ntpr=100,
> /
> ----------------
>
> unfortunately the mdout file contained nonzero EGB component which is wrong
> as with igb=6 this component should be zero.
>
>
> -----------
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1699 2.2518E+01 9.0334E-05 1.8502E-04 H5 16
>
> BOND = 0.2444 ANGLE = 0.1171 DIHED =
> 0.0070
> VDWAALS = -0.7541 EEL = 0.2895 EGB =
> 19.7516
> 1-4 VDW = 3.9462 1-4 EEL = -1.0835 RESTRAINT =
> 0.0000
>
> -----------
>
> This pmemd.cuda problem appears just for minimization. For MD it is OK
> (i.e. no EGB term is written in mdout)
>
>
> I tested also sander and cpu version of pmemd (see below) and there is
> everything OK so it is clearly
> just problem of pmemd.cuda.
>
>
> *** CPU pmemd output (minimization with above written settings)
> -------------------------
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1181 2.6109E+00 8.2061E-05 1.8709E-04 H5 16
>
> BOND = 0.1555 ANGLE = 0.1104 DIHED =
> 0.0065
> VDWAALS = -0.7525 EEL = 0.3077 EGB =
> 0.0000
> 1-4 VDW = 3.8767 1-4 EEL = -1.0935 RESTRAINT =
> 0.0000
>
> -------------------------
>
>
> *** sander output (minimization with above written settings)
> ----------------
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1181 2.6109E+00 8.2061E-05 1.8709E-04 H5 16
>
> BOND = 0.1555 ANGLE = 0.1104 DIHED =
> 0.0065
> VDWAALS = -0.7525 EEL = 0.3077 EGB =
> 0.0000
> 1-4 VDW = 3.8767 1-4 EEL = -1.0935 RESTRAINT =
> 0.0000
>
> ----------------
>
> Best wishes,
>
> Marek
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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Received on Thu Feb 09 2017 - 08:00:04 PST
