From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Feb 17 2017 - 14:49:07 CST
Hello,
I am trying to build NAMD 2.12 with the patch for running REST2
simulations, as described by the following paper
http://www.sciencedirect.com/science/article/pii/S001046551500329X
I have previously done this with NAMD 2.10 and it has worked fine. However,
with NAMD 2.12 I am getting errors (given below) when trying to run the
rest2.patch file. Has anyone been able to get it to work with NAMD 2.12?
Thanks and regards,
Chitrak.
patch -p1 <rest2.patch
(Stripping trailing CRs from patch.)
patching file Make.depends
Hunk #1 succeeded at 2816 with fuzz 2 (offset 267 lines).
(Stripping trailing CRs from patch.)
patching file Makefile
Hunk #1 succeeded at 169 (offset 12 lines).
(Stripping trailing CRs from patch.)
patching file src/ComputeAngles.C
Hunk #1 succeeded at 142 (offset 22 lines).
(Stripping trailing CRs from patch.)
patching file src/ComputeHomeTuples.h
(Stripping trailing CRs from patch.)
patching file src/ComputeNonbondedBase.h
Hunk #1 succeeded at 133 (offset 3 lines).
Hunk #2 succeeded at 146 (offset 3 lines).
Hunk #3 succeeded at 178 (offset 3 lines).
Hunk #4 succeeded at 217 (offset 3 lines).
Hunk #5 FAILED at 245.
Hunk #6 FAILED at 363.
Hunk #7 succeeded at 1714 (offset 67 lines).
Hunk #8 succeeded at 1724 (offset 67 lines).
2 out of 8 hunks FAILED -- saving rejects to file src/ComputeNonbondedBase.h.rej
(Stripping trailing CRs from patch.)
patching file src/ComputeNonbondedBase2.h
Hunk #1 succeeded at 92 with fuzz 1 (offset 17 lines).
Hunk #2 succeeded at 174 with fuzz 2 (offset 18 lines).
Hunk #3 succeeded at 193 (offset 19 lines).
Hunk #4 succeeded at 201 (offset 19 lines).
Hunk #5 succeeded at 210 with fuzz 1 (offset 19 lines).
Hunk #6 succeeded at 438 (offset 21 lines).
(Stripping trailing CRs from patch.)
patching file src/ComputeNonbondedSPT.C
(Stripping trailing CRs from patch.)
patching file src/ComputeNonbondedUtil.C
Hunk #1 succeeded at 115 (offset 28 lines).
Hunk #2 succeeded at 131 (offset 26 lines).
Hunk #3 succeeded at 303 with fuzz 2 (offset 31 lines).
Hunk #4 succeeded at 431 (offset 29 lines).
(Stripping trailing CRs from patch.)
patching file src/ComputeNonbondedUtil.h
Hunk #1 succeeded at 373 (offset 50 lines).
Hunk #2 succeeded at 480 (offset 56 lines).
(Stripping trailing CRs from patch.)
patching file src/ComputePme.C
Hunk #1 FAILED at 459.
Hunk #2 succeeded at 849 (offset 56 lines).
Hunk #3 succeeded at 903 (offset 62 lines).
Hunk #4 succeeded at 2639 (offset 69 lines).
Hunk #5 succeeded at 3064 (offset 133 lines).
Hunk #6 succeeded at 3113 (offset 133 lines).
Hunk #7 succeeded at 3125 (offset 133 lines).
Hunk #8 FAILED at 3020.
Hunk #9 FAILED at 3704.
Hunk #10 succeeded at 4102 (offset 285 lines).
Hunk #11 succeeded at 4224 (offset 288 lines).
3 out of 11 hunks FAILED -- saving rejects to file src/ComputePme.C.rej
(Stripping trailing CRs from patch.)
patching file src/ComputePme.h
Hunk #1 FAILED at 47.
1 out of 1 hunk FAILED -- saving rejects to file src/ComputePme.h.rej
(Stripping trailing CRs from patch.)
patching file src/ComputeSelfTuples.h
(Stripping trailing CRs from patch.)
patching file src/Controller.h
Hunk #1 succeeded at 239 with fuzz 1 (offset 34 lines).
(Stripping trailing CRs from patch.)
patching file src/Molecule.C
Hunk #1 succeeded at 299 (offset -15 lines).
Hunk #2 succeeded at 654 with fuzz 2 (offset -9 lines).
Hunk #3 succeeded at 5432 (offset 183 lines).
Hunk #4 succeeded at 5901 (offset 245 lines).
Hunk #5 FAILED at 8372.
1 out of 5 hunks FAILED -- saving rejects to file src/Molecule.C.rej
(Stripping trailing CRs from patch.)
patching file src/Molecule.h
Hunk #1 succeeded at 342 (offset 16 lines).
Hunk #2 succeeded at 903 (offset 184 lines).
Hunk #3 succeeded at 1330 with fuzz 1 (offset 232 lines).
(Stripping trailing CRs from patch.)
patching file src/NamdState.C
Hunk #1 succeeded at 112 (offset 1 line).
Hunk #2 succeeded at 506 (offset 25 lines).
Hunk #3 succeeded at 689 (offset 54 lines).
(Stripping trailing CRs from patch.)
patching file src/Sequencer.C
Hunk #1 succeeded at 274 (offset 17 lines).
(Stripping trailing CRs from patch.)
patching file src/SimParameters.C
Hunk #1 FAILED at 307.
Hunk #2 succeeded at 1104 (offset 12 lines).
Hunk #3 FAILED at 3204.
Hunk #4 succeeded at 4952 (offset 422 lines).
2 out of 4 hunks FAILED -- saving rejects to file src/SimParameters.C.rej
(Stripping trailing CRs from patch.)
patching file src/SimParameters.h
Hunk #1 succeeded at 422 (offset 9 lines).
(Stripping trailing CRs from patch.)
patching file src/WorkDistrib.C
Hunk #1 succeeded at 790 with fuzz 1 (offset 18 lines).
Hunk #2 FAILED at 818.
1 out of 2 hunks FAILED -- saving rejects to file src/WorkDistrib.C.rej
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