Hello Ross,
thanks for prompt and clear answer !
Best wishes,
Marek
Dne Thu, 14 Jul 2011 19:24:49 +0200 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Jul 14 2011 - 11:00:02 PDT
