Hi Marek,
Can you post the input and mdout file please. Also does the EGB value change during the minimization or is it always constant?
All the best
Ross
> On Feb 9, 2017, at 10:58, Marek Maly <marek.maly.ujep.cz> wrote:
>
> Hi Ross,
>
> with DPFP version is the same problem,
> here is the part of the DPFP minim. output.
>
> ---------------------------
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1084 2.2518E+01 9.2737E-05 2.1610E-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
>
>
> ---------------------------
>
> Marek
>
>
>
>
>
> Dne Thu, 09 Feb 2017 16:43:18 +0100 Ross Walker <ross.rosswalker.co.uk> napsal/-a:
>
>> 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
>>>
>>>
>>> --
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Received on Thu Feb 09 2017 - 09:00:03 PST
