Dear Rajeswari,
I guess that the best place to discuss this is PLUMED mailing list.
I guess that what happened there is, for some reason, there must be a
problem
in your Makefile. In my case I have a line like
AMBERBUILDFLAGS=-DAMBER
which instructs the added plumed code to compile the specific,
amber-related, features.
Check if you have it but please, consider to move this discussion on PLUMED
mailing
list where you might get more support.
Best regards,
Davide
On Thu, Dec 13, 2012 at 10:26 AM, Rajeswari A.
<rajeswari.biotech.gmail.com>wrote:
> Hello sir,
> I tried plumed 1.3 with amber 11 and the serial version installed fine with
> no error and the testing also fine. I have a doubt. In the plumed tutorial
> it was mentioned that the present version of PLUMED is fully compatible
> with GROMACS, DL POLY, AMBER and LAMMPS for parallel simulations. but when
> i tried to configure and make amber in parallel (after successful
> installation of serial version with plumed) it says an error.
>
> metadyn.c:1120:1: error: expected identifier or ‘(’ before ‘{’ token
> make[1]: *** [metadyn.o] Error 1
> make[1]: Leaving directory `/usr/local/amber11/src/sander'
> make: *** [parallel] Error 2
>
> Please clarify this sir. how to run metadynamics in sander.MPI?
>
> Thank you.
>
> On Mon, Dec 10, 2012 at 8:10 PM, Rajeswari A.
> <rajeswari.biotech.gmail.com>wrote:
>
> > 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
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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Received on Thu Dec 13 2012 - 02:00:02 PST
