Re: [AMBER] PLUMED patching with AMBER

From: Giovanni Bussi <giovanni.bussi.gmail.com>
Date: Sat, 14 Nov 2015 17:48:59 +0100

You should set it in your shell before running amber eg:

export PLUMED_KERNEL=/path



Inviato da iPhone

> Il giorno 14/nov/2015, alle ore 13:57, Sanjib Paul <sanjib88paul.gmail.com> ha scritto:
>
> Hello Giovanni,
> Environment variable PLUMED_KERNEL is properly set in
> that file. I have checked that. I am sending you that file. Do I have to
> set this path anywhere else?
>
> Thanking you.
>
> Sanjib
>
> On Fri, Nov 13, 2015 at 8:48 PM, Giovanni Bussi <giovanni.bussi.gmail.com>
> wrote:
>
>> Look for a file named libplumedKernel.so and set the env var PLUMED_KERNEL
>> to the full path of that file
>>
>> Giovanni
>>
>> On Fri, Nov 13, 2015 at 1:06 PM, Sanjib Paul <sanjib88paul.gmail.com>
>> wrote:
>>
>>> Hii,
>>> Thank you very much both of you. Initially I was using AmberTools14
>>> along with Amber14. Now I have upgraded AmberTools14 to AmberTools15.
>> Then
>>> I have installed mpi version of sander. I have also successfully
>> installed
>>> PLUMED. During installation of PLUMED I used '--prefix' flag to install
>> it
>>> my own directory not in system directory. Now when I going to run sander
>>> including two extra variables (plumed=1, plumedfile = 'plumed.dat') in
>>> input file I am getting following error message.
>>>
>>> *+++ ERROR: you are trying to use plumed, but it is not available +++*
>>> *+++ Check your PLUMED_KERNEL environment variable +++*
>>>
>>> From PLUMED website I have come to know that there is a file named '
>>> *modulefile*' in '*$prefix/lib/plumed/src/lib*' by editing which I can
>> set
>>> these environment variables. So I checked 'modulefile and noticed
>>> everything is all right there. What should I do to overcome this problem?
>>> Please help me out.
>>>
>>> Thanking you.
>>> Sanjib
>>>
>>> On Thu, Nov 12, 2015 at 10:15 PM, Jason Swails <jason.swails.gmail.com>
>>> wrote:
>>>
>>>> On Thu, Nov 12, 2015 at 11:35 AM, Giovanni Bussi <
>>> giovanni.bussi.gmail.com
>>>> wrote:
>>>>
>>>>> Jason, you are right.
>>>>>
>>>>> Ambertools 15 comes pre-patched with plumed, with a procedure that is
>>>>> equivalent to doing:
>>>>> plumed patch --runtime -p
>>>>>
>>>>> However, as far as I understood Sanjib is using Amber 14.
>>>>
>>>> ‚ÄčAmber 14 currently runs alongside AmberTools 15. Unfortunately the
>>>> meaning of "Amber 14" is a little ambiguous given the staggered release
>>>> schedule of Amber and AmberTools. I suspect that Sanjib is actually
>>>> running AmberTools 15 alongside a copy of Amber 14.
>>>>
>>>> So if Sanjib *is* using AmberTools 14, the best approach is to use
>>>> "./update_amber --upgrade" to upgrade to AmberTools 15, and then Plumed
>>>> should just work.
>>>>
>>>> All the best,
>>>> Jason
>>>>
>>>> --
>>>> Jason M. Swails
>>>> BioMaPS,
>>>> Rutgers University
>>>> Postdoctoral Researcher
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Received on Sat Nov 14 2015 - 09:00:04 PST
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