Re: [AMBER] problem

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 17 Jun 2015 08:27:10 -0600

Hi,

Usual debugging advice in this situation is to run the same simulation on
CPU (perhaps reducing nstlim) and see if that works. Also you may want to
check your initial coordinates using cpptraj's 'checkstructure' command
since the GPU code is a little more sensitive to bad initial configurations.

-Dan

On Wed, Jun 17, 2015 at 7:52 AM, zayan alhalabi <zayan82at.hotmail.com>
wrote:

> hello,
>
> iam simulating protein with peptide and cofactor inside
>
>
> when i run the equilbration stage
>
> command
> :pmemd.cuda -O -i md1.in -o Heat_md1.out -p cplx-sol.prmtop -c
> cplx_Emin2.rst -r Heat_md1.rst -ref cplx_Emin2.rst -x Heat_md1.mdcrd
> -inf equil1.inf
>
>
> the input file md1.in is
>
> heat up: 100ps MD with res on Protein
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 50000, dt = 0.002
> ioutfm = 1,
> ntpr = 5000, ntwx = 5000, ntwr = 5000
> /
> Keep PROTEIN fixed
> 10.0
> RES 1 281
> END
>
> i got this error :
>
> Error: unspecified launch failure launching kernel kNLSkinTest
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>
> could you please suggest any solution
> thanks
>
>
>
>
>
>
>
>
> Zayan AlhalabiInstitute of PharmacyMartin-Luther-Universit├Ąt
> Halle-WittenbergWolfgang-Langenbeck-Str. 406120 Halle (Saale), Germany
> Tel +49 345 55 25194
>
>
>
>
> E.mail zayan.alhalabi.pharmazie.uni-halle.de
>
>
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jun 17 2015 - 07:30:05 PDT
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