Hi Marek,
Unfortunately none of the NCSU features currently work with PMEMD either the
CPU or GPU versions. Unfortunately the format of the ncsu input files, not
having a switch in the cntrl namelist like all the other options in sander,
means that it is very hard to trap usage of NCSU options.
For the moment you will need to use Sander I am afraid. If NSF chooses to
renew my SI2-SSE funding then this will become possible, both GPU support in
Sander and additional features in pmemd. So cross your fingers (and toes!).
All the best
Ross
> -----Original Message-----
> From: Marek Maly [mailto:marek.maly.ujep.cz]
> Sent: Thursday, July 14, 2011 9:51 AM
> To: amber.ambermd.org
> Subject: [AMBER] Steered MD using pmemd.cuda ?
>
> Hello all,
>
> my colleague asked me if it is possible to do Steered MD using Amber
> GPU implementation which means for the moment pmemd.cuda. I didn't
> use this technique till now so I tried just simple test with sample
> input
> code
> (page 126 of Amber11 manual) below is the full input. This input was
> accepted
> and simulation was performed without any error but reqested "smd.txt"
> was
> not created
> so I am not sure if "ncsu_smd" part of my input was not simply ignored
> by
> pmemd.cuda,
> although I found the full input info written in *.out file.
>
>
> Thanks in advance for relevant comments !
>
> Best wishes,
>
> Marek Maly
>
>
> heat ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=250000,dt=0.002,
> ntc=2,ntf=2,iwrap=1,ioutfm=1,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> ig=-1,
> temp0=310.0,
> /
>
> ncsu_smd
> output_file = 'smd.txt'
> output_freq = 50
> variable
> type = DISTANCE
> i = (5, 9)
> path = (X, 3.0) path_mode = LINES
> harm = (10.0)
> end variable
> end ncsu_smd
>
>
>
>
>
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Received on Thu Jul 14 2011 - 10:30:03 PDT
