accomp lin wrote:
<http://www.mdbbs.org/tag-pull.html>
hi everyone,
I;m using umbrella sampling to calculate PMF
My system is DPPC + water + protein
In pull.ppa, I set runtype = umbrella ，reftype = com_t0，
K1 = 5000 ，Pos1 = 0.0 0.0 6.0
However this came out when I finally type mdrun :
Reading parameter file pull.ppa
' for variable verbose, using 'no'
Next time use one of : 'no' 'yes'
' for variable runtype, using 'afm'
Next time use one of : 'afm' 'constraint' 'umbrella'
' for variable reftype, using 'com'
Next time use one of ; 'com' 'com_t0' 'dynamic' 'dynamic_t0'
.....................
.....................
.....................
Then something is badly formatted in the file. Perhaps it was edited on a
Windows machine and has hidden formatting characters?
——————————————————————————————
program mdrun, VERSION 3.3.3
source code file: pullinit.c, line: 215
Fatal error:
in the index fileGN
——————————————————————————————
It seems that mdrun doesn't recognize what I set in pull.ppa
And I don't know what's wrong with my index file, it looks all right to me.
So, can any body tell me what is going on?
Could also be related to the same formatting issues you're seeing with your .ppa
file.
-Justin
Thanks!
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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