The restraints are during the eq. step and are being removed in the
production run.
Thanks a lot
Arik
On 8/11/2011 4:06 PM, Ross Walker wrote:
> Yeap... This is the NTB=2, ntr=1 bug. The fix really is coming soon.
>
> As I say for now either do not use restraints (why do you want restraints
> after the equilibration anyway?) or set ntb=1 and run with NVT.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: arikcohen [mailto:arikcohen.ucla.edu]
>> Sent: Thursday, August 11, 2011 3:54 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] unspecified launch failure launching kernel
>> kCalculateMolecularVirial
>>
>> Sorry, here is the eq.in
>>
>> equilibration run (0 - 2 ns)
>> &cntrl
>> imin=0, ! No minimization, plain MD(default)
>> irest=1, ! restart calculation
>> ntx=5, ! Read X and V formatted, if ntb> 0 read
>> box,
>> use V if irest = 1
>> ntb=2, ! Use pbc Pressure = const
>> pres0=1.0, ! Reference pressure
>> ntp=1, ! constant pressure dynamics
>> taup=2.0, ! Pressure relaxation time
>> cut=10, ! Non-bonded interaction cutoff
>> ntc=2, ! SHAKE: Constrain bonds involving H atoms
>> ntf=2, ! Typically ntf=ntc enable TIP3P constrain
>> tempi=300.0, temp0=300.0, ! Initial and final(reference) temperature if
>> ntt>0
>> ntt=3, ! Switch temperature scaling (3 Use Langevin
>> dynamics)
>> gamma_ln=1.0, ! Collision frequency for Langevin dynamics
>> nstlim=1000000, dt=.002, ! Number of MD steps and step size(in ps)
>> ntpr=100, ! Print energy every
>> ntwx=100, ! Print coor every
>> ntwr=500, ! Print for restart option every
>> ntr=1, ! Restrain atoms(cartesian space) using
>> harmonic potentail
>> &end
>> Group input for restrained atoms
>> 30
>> RES 1 8
>> RES 10
>> RES 12 47
>> RES 49
>> RES 51 99
>> RES 101 126
>> RES 128 199
>> RES 201 220
>> RES 222 248
>> END
>> END
>>
>> Thanks a lot again,
>>
>> Arik
>>
>> On 8/11/2011 3:12 PM, Ross Walker wrote:
>>> Hi Arik,
>>>
>>> Please send you input files. I suspect the bug is NPT + restraints
>> which is
>>> fixed in our development tree. Just waiting some final testing before
>>> release.
>>>
>>> For now you can run NVT and you should be fine.
>>>
>>> All the best
>>> Ross
>>>
>>>> -----Original Message-----
>>>> From: arikcohen [mailto:arikcohen.ucla.edu]
>>>> Sent: Thursday, August 11, 2011 3:05 PM
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] unspecified launch failure launching kernel
>>>> kCalculateMolecularVirial
>>>>
>>>> No. just a regular enzyme-substrate calculation.
>>>>
>>>> Arik
>>>>
>>>> On 8/11/2011 3:03 PM, Scott Le Grand wrote:
>>>>> Organic solvent or lipid bilayer simulation by any chance?
>>>>> On Aug 11, 2011 2:59 PM, "arikcohen"<arikcohen.ucla.edu> wrote:
>>>>>> Dear Users,
>>>>>>
>>>>>> While running on a GPU cluster I encountering from time time the
>>>>>> following persistent error:
>>>>>>
>>>>>> *unspecified launch failure launching kernel
>>>> kCalculateMolecularVirial*
>>>>>> I would be most thankful for any help/suggestion you might have.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Arik
>>>>>>
>>>>>>
>>>>>>
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Received on Thu Aug 11 2011 - 17:30:02 PDT
