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----
vlimit exceeded for step 218 ; vmax = 22.6949147823007
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 3 15 61 62
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
-----------------------------------------------------------------------
I did not understand why I am getting this error message. I have
checked out the initial .pdb files of ggcc and igigicic to be sure that
the procedure I have followed is right. When I checked out the
initial .pdb files of ggcc and igigicic using ambpdb, it is what I
expected: The atoms are exactly the same except the transformed atoms;
namely, -O-(DH)2 tranforms to -N-H2.
So, then I thought to run the same simulation in AMBER 8. I have created
the necessary .prmtop/.inpcrd files using exactly the same modified force
field file (.frcmod). Then, I ran a simulation (but not heating). Here is
the script used to do this simulation:
--------------------- runsim ---------------------------------------
#!/bin/csh -f
set lambda = 0.50
set sander = "/home/yildirim/bin/sander.mod.a8.new"
cat > mdin <<EOF
1 ps MD
&cntrl
imin = 0,
irest = 0, ntx = 1,
ntb = 1, cut = 8,
ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0, ig=233,
ntp=0,taup=2.0,pres0=1,
ntt = 3, gamma_ln = 1.0,
nstlim = 1000000, dt = 0.001, nscm = 1000, nrespa=1,
ntpr = 100, ntwx = 1000, ntwr = 1000,
icfe=2, klambda=6, clambda=$lambda
/
EOF
$sander -O -i mdin -p ggcc_pert.prmtop -c ggcc_pert.inpcrd -o \
ggcc.out -r ggcc.rst -x ggcc.mdcrd < /dev/null || goto error
exit(0)
echo " ${0}: Program error"
exit(1)
-------------------------------------------------------------
This simulation did not give any error message. I stopped it at 500th ps.
So, I decided that my new mix. function is working fine. I used the same
script (except, now the sander is sander.amber9.new) to do the same
simulation using AMBER 9. Here is the script I used:
---------------------------- runsim ----------------------------
#!/bin/csh -f
set lambda = 0.5
set sander = "/home/yildirim/bin/sander.amber9.new"
set mpi = "/home/yildirim/bin/perl/mpi"
/bin/rm -f mdin groups mdcrd restrt
cat > mdin <<EOF
1 ns simulation
&cntrl
imin=0,
ntx=1,irest=0,
ntpr=25,ntwr=1000,ntwx=1000,
ntc=2,ntf=2,ntb=1,cut=8,
igb=0,
ntr=0,
nstlim=1000000,dt=0.001,nscm=5000,nrespa=1,
ntt=0,tempi=300,temp0=300,ig=233,
ntp=0,taup=2.0,pres0=1,
icfe=2,klambda=6,clambda=$lambda
/
EOF
cat > groups <<EOF
-O -i mdin -p ggcc.prmtop -c inpcrd.min -o out.$lambda.p1
-O -i mdin -p igigicic.prmtop -c inpcrd.min -o out.$lambda.p2
EOF
$mpi -b -c mpirun 2 $sander -ng 2 -groupfile groups < /dev/null || goto
error
exit(0)
echo " ${0}: Program error"
exit(1)
------------------------------------------------------------------
This gave the same error at the end, and the output files have very
big values (as follows):
.
.
.
NSTEP = 1200 TIME(PS) = 1.200 TEMP(K) = NaN PRESS =
0.0
Etot = NaN EKtot = NaN EPtot = NaN
BOND = 643343.9308 ANGLE = 8405.3473 DIHED =
1101.6252
1-4 NB = 879.5059 1-4 EEL = -284.3524 VDWAALS =
3943.2851
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = NaN
Ewald error estimate: NaN
--------------------------------------------------------------------------
----
.
.
.
I am not sure why I am ending up with this kind of an error. I
first thought that the modified .frcmod might be the reason, but this
mod.frcmod file is working fine with AMBER 8. I have checked out the
.mdcrd trajectories, and the -NH2 and -O-(DH)2 parts of the structure is
doing really weird stuff. So, I am thinking that something in
'multisander' is creating this error, but I donno why and how.
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