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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Dec 13 2012 - 01:30:02 PST
