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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>> http://www.opera.com/mail/
>>
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Received on Thu Feb 09 2017 - 08:00:05 PST
