Re: [AMBER] &ewald skinnb=2.0d0 /

From: Ϳ־Ƽ <tuzhiping711.gmail.com>
Date: Tue, 2 Jul 2013 11:25:35 +0800

|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.3
|
| 04/24/2013
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------

|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2012, (In review).
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------

|------------------- GPU DEVICE INFO --------------------
|
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 6143 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|--------------------------------------------------------



2013/7/2 Scott Le Grand <varelse2005.gmail.com>

> What kind of GPU are your running this on?
>
>
>
> On Mon, Jul 1, 2013 at 7:47 PM, Ϳ־Ƽ <tuzhiping711.gmail.com> wrote:
>
> > Dear all,
> > Im using amber12 pmemd.cuda_SPFP( Version 12.3) to run MD simulation to
> > study the protein folding problem. But the running process is always
> > terminated soon. There was nothing error in the md2.out. The log.txt
> > exports: Nonbond cells need to be recalculated, restart simulation from
> > previous checkpoint with a higher value for skinnb.when I restarted it ,
> > this happened again after some time.I find the skinnb
> > default is 2.0 angstrom,but when I added *&ewald skinnb=3.0d0 / *to the
> > md2.in file,this error didn't happen, How does the skinnb value affect
> the
> > motion ?
> >
> > Any help will be appreciate. Thanks a lot.
> >
> > Yours
> > Tu Zhiping
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 01 2013 - 20:30:03 PDT
Custom Search