Dear Jason Swails
my previous error was removed.
Now, when I use mpirun -np 2 $AMBERHOME/bin/sander.MPI -ng 2 -groupfile
min.group & , I encounter with
Running multisander version of sander amber10
Total processors = 2
Number of groups = 2
forrtl: severe (24): end-of-file during read, unit 5, file /home/free_1_0.1/
min_v1.in, line 13, position 0
Image PC Routine Line
Source
sander.MPI 0000000000B4043A Unknown Unknown Unknown
sander.MPI 0000000000B3EF36 Unknown Unknown Unknown
sander.MPI 0000000000AE25E0 Unknown Unknown Unknown
sander.MPI 0000000000A8484E Unknown Unknown Unknown
sander.MPI 0000000000A83D8F Unknown Unknown Unknown
sander.MPI 0000000000AB4057 Unknown Unknown Unknown
sander.MPI 00000000004E8545 Unknown Unknown Unknown
sander.MPI 00000000004BAD86 Unknown Unknown Unknown
sander.MPI 00000000004BA935 Unknown Unknown Unknown
sander.MPI 0000000000405A7C Unknown Unknown Unknown
libc.so.6 00000039C5C1EC5D Unknown Unknown Unknown
sander.MPI 0000000000405979 Unknown Unknown Unknown
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 26505 failed on node n0 (217.218.85.50) with exit status 24.
Output file is as follows:
| Run on 02/07/2012 at 19:19:00
[-O]verwriting output
File Assignments:
| MDIN: free_1_min_v0_0.1.in
| MDOUT: free_tg_1_min_v0_0.1.out
|INPCRD: free_tg_1_v0_0.1.inpcrd
| PARM: free_tg_1_v0_0.1.prmtop
|RESTRT: free_tg_1_min_v0_0.1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: free_tg_1_min_v0_0.1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
free_1_min_v0_0.1
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1
ifsc = 0,
crgmask ="
scmask ="
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
how to fix it?
any help will highly appreciated.
On Mon, Feb 6, 2012 at 9:43 PM, leila karami <karami.leila1.gmail.com>wrote:
> Dear Jason Swails
>
> Thanks for your attention
>
> In min_v1.in file, crgmask defined twice, Because I want to
> investigate free energy changes in mutation of the dna (GC base pair
> ---> AT base pair). one for G base and the other for C base.
>
> how to define crgmask only once?
>
> You should probably put masks in quotes.
> crgmask = ":DG9.O6,H1,N2,H21,H22"
> is it true?
>
>
> On 2/6/12, Jason Swails <jason.swails.gmail.com> wrote:
> > On Mon, Feb 6, 2012 at 10:36 AM, leila karami
> > <karami.leila1.gmail.com>wrote:
> >
> >> Dear amber users
> >>
> >> I am trying to perform thermodynamic integration using soft core
> >> potentials
> >> (like tutorial A9).
> >>
> >> I want to investigate free energy changes in mutation of the dna (GC
> base
> >> pair ---> AT base pair).
> >>
> >> I do first step (removing charge of G9 and C18).
> >>
> >> But after mpirun -np 4 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile
> >> min.group,I am faced with
> >> the error in reading namelist cntrl.
> >>
> >> my input files are as follows:
> >>
> >> min_vo.in
> >>
> >> &cntrl
> >> imin = 1, ntx = 1,
> >> maxcyc = 2000, ncyc = 1000,
> >> ntpr = 100,
> >> ntf = 2, ntc = 2,
> >> ntb = 1, cut = 10.0,
> >> icfe = 1, clambda = 0.1
> >> ifsc = 0,
> >> crgmask ="
> >> scmask ="
> >> /
> >>
> >> min_v1.in
> >>
> >> &cntrl
> >> imin = 1, ntx = 1,
> >> maxcyc = 2000, ncyc = 1000,
> >> ntpr = 100,
> >> ntf = 2, ntc = 2,
> >> ntb = 1, cut = 10.0,
> >> icfe = 1, clambda = 0.1
> >> ifsc = 0,
> >> crgmask = :DG9.O6,H1,N2,H21,H22
> >> crgmask = :DC18. N4,H41,H42,H5
> >>
> >
> > Why do you have crgmask defined twice? Also, you should probably put
> masks
> > in quotes (single or double, I don't think it matters).
> >
> >
> >> scmask ="
> >> /
> >>
> >> Any help will highly appreciated.
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
Received on Tue Feb 07 2012 - 00:30:02 PST
