Dear Davide,
I thank you very much for your quick and elaborate reply. Surely i will try
your suggestions and reply you.
Thanks a lot
Rajeswari
On Mon, Dec 10, 2012 at 7:44 PM, davide branduardi <
davide.branduardi.gmail.com> wrote:
> 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
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Dec 10 2012 - 07:00:03 PST
