From: Sourav Ray (souravray90_at_gmail.com)
Date: Thu Apr 16 2015 - 06:27:30 CDT
I think the problem is box distortion, there was no such issue while doing
the simulation with a single peptide. I can start from recent checkpoint
but ultimately it's not a permanent fix as I have to keep on doing it.
On Wed, Apr 15, 2015 at 7:54 PM, Prathit Chatterjee <pc20apr_at_yahoo.co.in>
wrote:
> Please try to restart from the recent checkpoint as suggested in the
> error, and see if it works.
>
> Best
> Prathit
>
>
>
>
> On Wednesday, 15 April 2015 7:35 PM, Sourav Ray <souravray90_at_gmail.com>
> wrote:
>
>
> I have resolved the error now. It requires application of the fix_martini
> script to run the system.
>
> However, currently I am facing this error now:
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> Even though useFlexibleCell is set to 'no' and my box dimensions cover the
> entire system. Moreover I have set the center correctly. Can anyone provide
> more insight please?
>
> On Wed, Apr 15, 2015 at 4:21 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
>
> I keep on getting similar errors like:
>
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR P5 P5 (ATOMS 1 2)
>
> I have shifted the peptide by 5, 7.5 and 10 angstroms to study the
> interaction between two molecules. Has anyone else here faced a similar
> error/situation?
>
> On Wed, Apr 15, 2015 at 4:09 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
>
> Hello
>
> Although I have been able to run single molecule coarse-grained
> simulation. I faced the following error while running two peptide
> equilibriation simulation.
>
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
>
> [0] Stack Traceback:
> [0:0] CmiAbort+0x5f [0xe8725f]
> [0:1] _Z8NAMD_diePKc+0x62 [0x663b9a]
> [0:2] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0x1de [0xc0d810]
> [0:3] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x190 [0xbb3e6e]
> [0:4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x3e5 [0xbb117d]
> [0:5] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
> [0xbb0cd1]
> [0:6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
> [0xbb5bca]
> [0:7] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
> [0:8] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
> [0:9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
> [0:10] TclInvokeStringCommand+0x88 [0xecef58]
> [0:11] [0xed1a70]
> [0:12] [0xf14853]
> [0:13] [0xf1a613]
> [0:14] TclEvalObjEx+0x86 [0xed36c6]
> [0:15] [0xedc61d]
> [0:16] [0xed1a70]
> [0:17] [0xed2e56]
> [0:18] Tcl_EvalEx+0x16 [0xed3636]
> [0:19] Tcl_FSEvalFileEx+0x151 [0xf35441]
> [0:20] Tcl_EvalFile+0x2e [0xf355fe]
> [0:21] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
> [0:22] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
> [0:23] main+0x3a [0x6684c2]
> [0:24] __libc_start_main+0xf5 [0x7f9c1c22bec5]
> [0:25] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
> Charm++ fatal error:
> FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR AC2v P5 (ATOMS 2 3)
>
> [0] Stack Traceback:
> [0:0] [0xe88055]
> [0:1] CmiAbort+0x9d [0xe8729d]
> [0:2] _Z8NAMD_diePKc+0x62 [0x663b9a]
> [0:3] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0x1de [0xc0d810]
> [0:4] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x190 [0xbb3e6e]
> [0:5] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x3e5 [0xbb117d]
> [0:6] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
> [0xbb0cd1]
> [0:7] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
> [0xbb5bca]
> [0:8] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
> [0:9] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
> [0:10] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
> [0:11] TclInvokeStringCommand+0x88 [0xecef58]
> [0:12] [0xed1a70]
> [0:13] [0xf14853]
> [0:14] [0xf1a613]
> [0:15] TclEvalObjEx+0x86 [0xed36c6]
> [0:16] [0xedc61d]
> [0:17] [0xed1a70]
> [0:18] [0xed2e56]
> [0:19] Tcl_EvalEx+0x16 [0xed3636]
> [0:20] Tcl_FSEvalFileEx+0x151 [0xf35441]
> [0:21] Tcl_EvalFile+0x2e [0xf355fe]
> [0:22] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
> [0:23] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
> [0:24] main+0x3a [0x6684c2]
> [0:25] __libc_start_main+0xf5 [0x7f9c1c22bec5]
> [0:26] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
> Aborted (core dumped)
>
> Regards
> Sourav Ray
>
>
>
>
>
>
>
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