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 - 16:00:03 PDT
