Dear All,
I have an explicit water system, similar to the DNA tutorial. I am doing
a perturbation on this system. I am trying to use the new sander
(ver. AMBER 9). I want to heat the system from 0 to 300 K. The new
sander's procedure is different than the old sander (AMBER 8). In the old
version, we were creating just one prmtop file which is called as pert.
prmtop file. In the new approach, two .prmtop files are created (for the
initial and final states seperately), and then a parallel run is done to
calculate the dv/dl values. But I am getting an error message when I try
to heat the system up. I have the following script:
----------------------- runsim_heating ---------------------
#!/bin/csh -f
set lambda = 0.50
set sander = "/home/yildirim/amber9/exe/sander"
set mpi = "/home/yildirim/bin/perl/mpi"
cat > mdin <<EOF
20ps MD with res on RNA - Heating
&cntrl
imin = 0,
irest = 0, ntx = 1,
ntb = 1, cut = 8,
ntr = 0,
ntc = 2, ntf = 2,
tempi = 0.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 10000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000,
icfe=2, klambda=6, clambda=0.5
/
Keep RNA fixed with weak restraints
10.0
RES 1 8
END
END
EOF
cat > groups <<EOF
-O -i mdin -p ggcc.prmtop -c inpcrd_min02.res -r ggcc_heating.rst -x
ggcc_heating.mdcrd -ref inpcrd_min02.res -o out.heating.$lambda.p1
-O -i mdin -p igigicic.prmtop -c inpcrd_min02.res -r igigicic_heating.rst
-x igigicic_heating.mdcrd -ref inpcrd_min02.res -o out.heating.$lambda.p2
EOF
$mpi -b -c mpirun 2 $sander -ng 2 -groupfile groups < /dev/null || goto
error
/bin/rm -f mdin groups
exit(0)
echo " ${0}: Program error"
exit(1)
----------------------------------------------------------------
Here, 'mpi' is a perl script which is finding the best machine in the
cluster and putting the jobs into those machines, which is working fine.
Here is the error message I am getting:
------------------------- error ----------------------------
arde20:/home/yildirim/ggcc_igigicic/lambda_0.50>runsim_heating
( mpirun -stdin /dev/null -np 2 -nolocal -machinefile /tmp/tmp.mpi.11175
/home/yildirim/amber9/exe/sander -ng 2 -groupfile groups; rm -f
/tmp/tmp.mpi.11175 ) &
running on arde08:1 arde10:1
arde20:/home/yildirim/ggcc_igigicic/lambda_0.50>
Unit 15 Error on OPEN: groups
Unit 15 Error on OPEN: groups
p0_15041: p4_error: : 1
Unit 15 Error on OPEN: groups
[0] MPI Abort by user Aborting program !
[0] Aborting program!
Killed by signal 2.
arde20:/home/yildirim/ggcc_igigicic/lambda_0.50>
-------------------------------------------------------------
The heating process works fine when I do it on just the initial system.
But when I use the 'icfe=2, klambda=6, clambda=0.5' or 'icfe=1,
klambda=6, clambda=0.5', then it is giving me the above error message.
Does that mean that we cannot heat the system with this new sander? Or am
I doing something wrong? Thanks in advance.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
---------------------------------------------------------------
Received on Wed Apr 05 2006 - 23:49:47 PDT
