Dear Rajeswari,
I am one of plumed developers and there are no project active from us
that involve amber12 (AFAIK). For that reason we just support only amber11.
Nevertheless you can try out to hack sander at your own peril. I did not
find any major problem in moving from
version 10 to 11 but I do not know about 12. Might be that it is as simple.
A good starting point is the following:
- take a old version of amber that is supported by plumed and make a test (
a simple umbrella sampling or metadynamics) on a simple system and store
the result.
-patch the new sander code with plumed: check if all the procedure goes
well (i.e. do you get any FAIL for the patching? does the script find the
patch tool?). If you overlook this stage it might well be that the program
compiles but WITHOUT plumed!! This might be your case since it looks like
the command line is not recognized.
If it fails try to check the code (.rej files), compare the patched
previous version with actual sander and try to figure out an equivalent
position for the plumed calls in the source (they are not many, probably 3
or 4, it should not be a big deal) and try to patch the code "by hand"
-make the test and see if you get any PLUMED.OUT file in output and if your
outputs coincide with the previous version.
Hope it helps!
Good luck!
Davide
PS: a useful thing is to post these question in plumed-user mailing list as
well!
On Mon, Dec 10, 2012 at 11:32 AM, Rajeswari A.
<rajeswari.biotech.gmail.com>wrote:
> Dear amberusers,
> I want to know whether Plumed 1.3 is compatible with amber12? i installed
> amber 12 along with plumed1.3. During installation there was no error
> message. But all plumed tests were failed and for my own system when i run
> sander with plumed, it says "error in reading namelist cntrl". my input
> file is below which has additional 2flags for plumed.
>
> &cntrl
> imin = 0, ntx = 7, irest = 1,
> ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
> ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> nstlim = 500000, dt =0.002,
> tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> plumed=1 , plumedfile=’plumed.dat’
> &end
>
> Waiting for your response!
>
> Thank you,
> Rajeswari A
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Dec 10 2012 - 06:30:02 PST
