AMBER input and REST2 leads to crash

From: Victor Zhao (
Date: Tue Sep 15 2020 - 00:53:42 CDT


I’ve previously run REST2 simulations using a PSF file prepared with c36m with no issues. The REST2 implementation is the one included with the download of NAMD (lib/replica/REST2). Now, when I try to run a REST2 simulation using an AMBER .prmtop file, I get the following crash (from the stdout/stderr log):

*** Error in `/n/home00/vzhao/opt/NAMD_2.14_Linux-x86_64-netlrts-smp-CUDA/namd2': free(): invalid next size (fast): 0x0000000013267df0 ***

A bunch of backtrace lines follow. As can be seen in the above error message, I am running replica exchange using the netlrts-smp-CUDA version of NAMD. When I look into the individual replica log files for the crash, I see the following:

Info: Reading solute scaling data from file: ../DHFR_wt_apo_equild_temper_helix.pdb
Info: Reading solute scaling flags from column: 4
[0] Stack Traceback:
  [0:0] 0x2af4c0aea207 gsignal
  [0:1] 0x2af4c0aeb8f8 abort
  [0:2] 0x2af4c0b2cd27
  [0:3] 0x2af4c0b35489
  [0:4] namd2 0xba12d2
  [0:5] namd2 0xbe788c
  [0:6] namd2 0xbeb828
  [0:7] namd2 0xd0b9ab
  [0:8] namd2 0x195b678 TclInvokeStringCommand
  [0:9] namd2 0x195e190
  [0:10] namd2 0x19a0f73
  [0:11] namd2 0x19a6d33
  [0:12] namd2 0x195fde6
  [0:13] namd2 0x1972844
  [0:14] namd2 0x195e190
  [0:15] namd2 0x195f576
  [0:16] namd2 0x195fd56
  [0:17] namd2 0x19c1b61
  [0:18] namd2 0x196ed4a
  [0:19] namd2 0x195e190
  [0:20] namd2 0x195f576
  [0:21] namd2 0x195fd56
  [0:22] namd2 0x19c1b61
  [0:23] namd2 0x19c1d1e
  [0:24] namd2 0xd08580
  [0:25] namd2 0x511210
  [0:26] 0x2af4c0ad63d5 __libc_start_main
  [0:27] namd2 0x4161a5

Seeing these crash messages, I am not sure how to proceed. The occurrence of the crash after the solute scaling file read suggests there’s something wrong there. I verified that my input files work in a normal (non-REST) simulation. Since my procedure to setup and run REST simulations worked previously with a psf input, I am wondering whether the issue is that my input files have been changed to the AMBER format (“amber yes”). Has anyone successfully run REST2 simulations using AMBER-format file inputs?

[As an aside, I encountered an issue where I cannot start new NAMD simulations using crd files written using the writecrd function in VMD. Instead, providing a PDB file to “coordinates” instead of using “ambercoor” works.]


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