Ok, thanks. By the way here is my input file:
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, ! Tipically ntf=ntc enable TIP3P constrain
tempi=300.0, temp0=300.0, ! Initial and final(reference) temperature if
ntt>0
ntt=3, ! Switch temperature scalling (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 again,
Arik
On 8/11/2011 3:28 PM, Ross Walker wrote:
> I assume you are using restraints as well?
>
> Just run production with NVT and NTT=1 - Really once you have equilibrated
> the density you should be fine to use a Berendsen thermostat and constant
> volume. You'll get much better performance to boot.
>
> The fix for NPT + restraints is coming. We are just checking things
> carefully before releasing a series of updates.
>
>> -----Original Message-----
>> From: arikcohen [mailto:arikcohen.ucla.edu]
>> Sent: Thursday, August 11, 2011 3:19 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] unspecified launch failure launching kernel
>> kCalculateMolecularVirial
>>
>> Hi Ross,
>>
>> Thanks for the fast replay. I should mention that i have encountered
>> this error several times now. The current one is a restart run of an
>> equilibration that run just fine also on GPU with the same condition of
>> constant pressure .
>>
>> Thanks a lot,
>>
>> 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 - 16:00:02 PDT
