Hi,
The main issues are here:
On Sun, Oct 12, 2014 at 8:15 AM, Yeng-Tseng Wang <c00jsw00.gmail.com> wrote:
> | AMD error all main parameters are 0.0 for Accelerated MD (AMD) or
> Windowed Accelerated MD (wAMD)
>
> Cannot match namelist object name pdhgt
> namelist read: misplaced = sign
> Cannot match namelist object name 830.00
> Cannot match namelist object name pdtune
> namelist read: misplaced = sign
> Cannot match namelist object name 3.20pdhgta
> namelist read: misplaced = sign
> Cannot match namelist object name 56599.00
> Cannot match namelist object name pdtunea
> namelist read: misplaced = sign
> Cannot match namelist object name 060.00
> STOP PMEMD Terminated Abnormally!
These are not the correct namelist variables for aMD. The namelist
variables you want are:
alphad: Dihedral energy alpha value.
ethreshd: Dihedral energy threshold value.
alphap: Potential energy alpha value.
ethreshp: Potential energy threshold value.
There is a mistake in the MDIN for tutorial A22 section 2 (which it
appears you are using). The Amber 14 manual has the correct
information (section 20.2). We will have to correct the tutorial -
thanks for the report.
-Dan
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--
-------------------------
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 Sun Oct 12 2014 - 10:00:07 PDT
