Dear Prof. Case
Link to the tutorial "
https://ambermd.org/tutorials/advanced/tutorial22/section1.php”
The Structure input files I used are "bpti-ff99SBi.prmtopp <
https://ambermd.org/tutorials/advanced/tutorial22/files/bpti-ff99SBi.prmtop>, bpti-ff99SBi.inpcrd <
https://ambermd.org/tutorials/advanced/tutorial22/files/bpti-ff99SBi.inpcrd>”
The input file I am referring to is "heat-wat.in <
http://heat-wat.in/>” which gets downloaded as "
https://ambermd.org/tutorials/advanced/tutorial22/files/md_wat.in”
——————————
Relax water
LET WATER MOVE
&cntrl
timlim = 999999., nmropt = 0, imin = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 500, ntwx = 500, ntwv = 0, ntwe = 0,
ntwr = 5000,
ntf = 2, ntb = 2,
cut = 10.0, nsnb = 20,
nstlim = 10000, nscm = 2500, iwrap = 1,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 200.0, tautp=0.5,
ntt = 1,
ntp =1 , taup = 1.0,
ntc = 2, tol = 0.00001,
ibelly=0, ntr=1,
restraintmask="!:WAT" , restraint_wt=10.0,
&end
/
——————————————————
I am able to successfully execute
$AMBERHOME/bin/pmemd.cuda -O -i min_wat.in -o min_wat.out -p ../*.prmtop -c ../*.inpcrd -r min_wat.rst -ref ../*.inpcrd
But when am try running the following command the run fails
$AMBERHOME/bin/pmemd.cuda -O -i md_wat.in -o md_wat.out -p ../*.prmtop -c ../1_/*.rst -r md_wat.rst -ref ../1_/*.rst
Run output is
At line 980 of file /opt/amber22_src/src/pmemd/src/mdin_ctrl_dat.F90 (unit = 5, file = 'md_wat.in')
Fortran runtime error: Cannot match namelist object name .
Error termination. Backtrace:
#0 0x7f31de94ad21 in ???
#1 0x7f31de94b869 in ???
#2 0x7f31de94c54f in ???
#3 0x7f31deb8a65d in ???
#4 0x7f31deb93ae7 in ???
#5 0x7f31deb93d0c in ???
#6 0x7f31deb93e67 in ???
#7 0x55c64aa10a51 in ???
#8 0x55c64aacbb82 in ???
#9 0x55c64aaac118 in ???
#10 0x55c64a9dd9ce in ???
#11 0x7f31de741082 in __libc_start_main
at ../csu/libc-start.c:308
#12 0x55c64a9f974d in ???
#13 0xffffffffffffffff in ???
Thanks for your help in advanced
Regards
Raghuvir
> On 11-May-2023, at 00:49, David A Case <david.case.rutgers.edu> wrote:
>
> On Wed, May 10, 2023, Raghuvir Pissurlenkar via AMBER wrote:
>
>> I am trying to execute the aMD tutorial
>
> Can you be more explicit? Which tutorial? In tutorial 6.3, I don't see any
> "md_wat.in" file. Since that is the file that has the namelist problem,
> it's probably best to post the actual file here, in any event.
>
> (Apologies if I am missing something that is actually in that tutorial.)
>
> ....dac
>
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Received on Wed May 10 2023 - 15:00:02 PDT
