hello:
I am trying to use the following two .in file for my NVT steps but
both of them failed with similar errors:
command:
mpiexec -np 6 $AMBERHOME/exe/sander.MPI -O -i heat.in -p bm.prmtop -c
mini2.rst -o heat.out -r heat.rst -x heat.mdcrd -ref mini2.rst
------------1.in--------------
heating gradually over 300ps
&cntrl
imin=0,irest=0,ntx=1,
nstlim=300000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
nmropt=1
/
Hold the 1-288 fixed
50.0
RES 1 288
&wt TYPE='TEMP0', istep1=0, istep2=300000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
END
----------fail-1.log---------
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2b59f9dea970
src_=0x2b59f9dea970 len_=157944
internal ABORT - process 0
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2adf68627b30
src_=0x2adf68627b30 len_=157968
internal ABORT - process 2
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2b927d5b2268
src_=0x2b927d5b2268 len_=157896
internal ABORT - process 1
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2aae7798e440
src_=0x2aae7798e440 len_=157896
-----------------2.in-------------------
heating gradually over 300ps
&cntrl
imin=0,irest=0,ntx=1,
nstlim=300000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ntr=1, restraintmask=':1-288',
restraint_wt=10.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=300000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
---------------fail-2.log------------
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2afc3e2b1970
src_=0x2afc3e2b1970 len_=157944
internal ABORT - process 0
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2ba962177268
src_=0x2ba962177268 len_=157896
internal ABORT - process 1
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2b4ddb67ab30
src_=0x2b4ddb67ab30 len_=157968
internal ABORT - process 2
Assertion failed in file helper_fns.c at line 335: 0
memcpy argument memory ranges overlap, dst_=0x2b24f2f80d08
src_=0x2b24f2f80d08 len_=157896
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Received on Fri Apr 13 2012 - 12:00:03 PDT
