Here it is [including prmtop and inpcrd files]
http://www.uschovna.cz/zasilka/LI8LMJ77FVS7L58Z-ZSL/
The EGB is changing during the minimization.
Best,
Marek
Dne Thu, 09 Feb 2017 17:43:07 +0100 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> 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 - 09:30:02 PST
