Try setting iwrap=0 in all your input files...
I am suspicious that molecules are getting wrapped but their constraints
aren't...
On Wed, Nov 9, 2011 at 1:07 AM, Giovanni Pavan <giovanni.pavan.supsi.ch>wrote:
> Dear all,
>
> I am running a simulation on a single C2050 GPU.
>
> The system is quite unconventional and composed by 9 single strand DNAs
> attached with a short tiol onto a surface of gold
>
> The system is created in order to have an equal spacing between each ssDNA
> (also in terms of periodic images).
>
> To do so the water box is created with 0 buffer in X and Y directions, and
> with opportune spacing along Z.
>
>
>
> The system seems to pass successfully the heating to 300K
>
> After that, I run NVT MD simulation in order to maintain the box dimensions
> constant.
>
> The simulation is divided into 1ns stages and here the gold surface is
> restrained with ntr=1 and a constant of 10.0.
>
> The 1st part of simulation (1ns - but this is true independently on the
> length of each stage) passes without problems , but when it goes to step 2
>
> Starting from RST1 I obtain the following message:
>
>
>
> Error: unspecified launch failure launching kernel kReduceForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>
>
>
> My input file is below. (# indicates a comment just to make it clear).
>
>
>
> equil SAM
>
> &cntrl
>
> imin=0,
>
> irest=0,
>
> ntx=1,
>
> nstlim=5000,
>
> dt=0.002,
>
> ntc=2,
>
> ntf=2,
>
> cut=8.0,
>
> ntb=2, #the run is actually an NVT,
>
> ntp=1, #this trick is used to monitor
>
> taup=999999999999999999999999999, #pressure and density
>
> ntpr=1000,
>
> ntwx=1000,
>
> ntt=3,
>
> gamma_ln=2.0,
>
> temp0=300,
>
> ntr=1,
>
> ig=-1,
>
> iwrap=1,
>
> ioutfm=1,
>
> /
>
> fix surface
>
> 10.0
>
>
> RES 1 5445
>
> END
>
> END
>
>
> END
>
>
>
> I need your help, since I don't understand if the problem is related to the
> system or to some problem with the GPU.
>
> (it seems more the 2nd case as from
> http://dev-archive.ambermd.org/201103/0019.html ).
>
> Maybe a problem due to a too short cutoff?
>
> I eagerly look forward to receive any comment from you.
>
> Best,
>
> Giovanni
>
>
>
> Dr. Giovanni Maria Pavan
>
>
>
> SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
>
> Centro Galleria 2, Manno 6928, Switzerland.
>
> e-mail: giovanni.pavan.supsi.ch
>
> skype: giovanni_pavan
>
> phone: +41 58 666 65 60
>
>
>
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Received on Wed Nov 09 2011 - 16:30:03 PST
