[Apbs-users] about the electrostatic energy of two helixes

[Wang L. <wa...@bi...>]

hi, everyone

      recently i am using APBS to calculate the electrostatic energy of 
different configurations of two helixes, i scan the energy across the 
six-dimensions, three translations and three rotations, i want to find the 
favorable reaction pathways of the dissociation of two helixes. since it 
needs huge calculations, so i write a shell script to automatize the job,
but some problems appears: 
 the script randomly stops without any error mesage after several hours.
at first i think it is lack of memory, so i move the job to run at node(64bit) 
with 16G memory and 4 cpu, every time i just submit one job at one node, the 
output of job show it costs memory about 2G, even so, the script stops too,

another little problem is every time i execute APBS *.in, the *.out file 
always appear "asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input."

i have test *.out with APBS's example output file, the results are the same, 
seems above error message doesn't affect the final result.


i paste the script, the input, the output here!

hope your reply!