From: Ling Wu (emilia.l.wu_at_gmail.com)
Date: Mon Aug 29 2011 - 09:55:45 CDT
Hi Glacomo,
Thanks a lot for your help!, here I copied all the information I have right now for the output error message,
and if the colvar can only restrain the center of mass of the water layer, is there any other way to do this with NAMD. I actually need not only restrain the water molecule, but also the lipid head group atoms and tail atoms, so it is impossible to do it atom by atom.
Thank you very much!
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 13603 ATOMS
Info: 11822 BONDS
Info: 17851 ANGLES
Info: 23352 DIHEDRALS
Info: 144 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 10425 RIGID BONDS
Info: 30384 DEGREES OF FREEDOM
Info: 4973 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 4973 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 78474.9 amu
Info: TOTAL CHARGE = 2.14577e-06 e
Info: MASS DENSITY = 1.10811 g/cm^3
Info: ATOM DENSITY = 0.115672 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 1.77335 s, 6.23213 MB of memory in use
Info: Startup phase 0 took 7.10487e-05 s, 6.23222 MB of memory in use
Info: Startup phase 1 took 0.031409 s, 9.64294 MB of memory in use
Info: Startup phase 2 took 0.000336885 s, 9.77924 MB of memory in use
Info: Startup phase 3 took 5.29289e-05 s, 9.77911 MB of memory in use
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 3 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (4) HAS 1321 ATOMS
Info: Startup phase 4 took 0.00933218 s, 11.6342 MB of memory in use
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 5 took 0.0011549 s, 12.345 MB of memory in use
Info: Startup phase 6 took 8.60691e-05 s, 12.3448 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.000139952 s, 12.3463 MB of memory in use
Info: CREATING 235 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2011-02-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100 [default]
colvars: # colvarsRestartFrequency = 1000 [default]
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "step6.1_equilbration.colvars.state".
colvars: The final output state file will be "step6.1_equilibration.colvars.state".
colvars: The trajectory file will be "step6.1_equilibration.colvars.traj".
colvars: Error: no collective variables defined.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0:0] CmiAbort+0x7b [0xbf1bd9]
[0:1] _Z8NAMD_diePKc+0x62 [0x535542]
[0:2] _ZN16colvarproxy_namd11fatal_errorERKSs+0x64 [0x97b41a]
[0:3] _ZN12colvarmodule11fatal_errorERKSs+0x18 [0x8bda48]
[0:4] _ZN12colvarmodule12init_colvarsERKSs+0x247 [0x8bf90d]
[0:5] _ZN12colvarmoduleC9EPKcP11colvarproxy+0xeea [0x8b54d8]
[0:6] _ZN12colvarmoduleC1EPKcP11colvarproxy+0x6 [0x8b6d54]
[0:7] _ZN16colvarproxy_namdC9Ev+0x39d [0x975089]
[0:8] _ZN16colvarproxy_namdC1Ev+0x6 [0x975a84]
[0:9] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x409 [0x5c3e93]
[0:10] _ZN4Node7startupEv+0x2c7 [0xa00191]
[0:11] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x9ffec6]
[0:12] CkDeliverMessageFree+0x21 [0xb2d373]
[0:13] _Z15_processHandlerPvP11CkCoreState+0x70b [0xb2c21b]
[0:14] CsdScheduleForever+0xa5 [0xbf87f3]
[0:15] CsdScheduler+0x1c [0xbf83f4]
[0:16] _ZN7BackEnd7suspendEv+0xb [0x53e3e1]
[0:17] _ZN9ScriptTcl9initcheckEv+0x80 [0xa7c364]
[0:18] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0xa78a94]
[0:19] TclInvokeStringCommand+0x91 [0xc26a58]
[0:20] /home2/emiliawu/NAMD_2.8_Linux-x86_64/namd2 [0xc5c8a8]
[0:21] Tcl_EvalEx+0x176 [0xc5ceeb]
[0:22] Tcl_EvalFile+0x134 [0xc548f4]
[0:23] _ZN9ScriptTcl4loadEPc+0x10 [0xa77e42]
[0:24] _Z18after_backend_initiPPc+0x448 [0x539cc8]
[0:25] main+0x3a [0x53984a]
[0:26] __libc_start_main+0xdb [0x3052d1c3fb]
[0:27] _ZNSt8ios_base4InitD1Ev+0x4a [0x534e3a]
Charm++ fatal error:
FATAL ERROR: Error in the collective variables module: exiting.
[0] Stack Traceback:
[0:0] /home2/emiliawu/NAMD_2.8_Linux-x86_64/namd2 [0xbf27e9]
[0:1] CmiAbort+0xb9 [0xbf1c17]
[0:2] _Z8NAMD_diePKc+0x62 [0x535542]
[0:3] _ZN16colvarproxy_namd11fatal_errorERKSs+0x64 [0x97b41a]
[0:4] _ZN12colvarmodule11fatal_errorERKSs+0x18 [0x8bda48]
[0:5] _ZN12colvarmodule12init_colvarsERKSs+0x247 [0x8bf90d]
[0:6] _ZN12colvarmoduleC9EPKcP11colvarproxy+0xeea [0x8b54d8]
[0:7] _ZN12colvarmoduleC1EPKcP11colvarproxy+0x6 [0x8b6d54]
[0:8] _ZN16colvarproxy_namdC9Ev+0x39d [0x975089]
[0:9] _ZN16colvarproxy_namdC1Ev+0x6 [0x975a84]
[0:10] _ZN10ComputeMgr14createComputesEP10ComputeMap+0x409 [0x5c3e93]
[0:11] _ZN4Node7startupEv+0x2c7 [0xa00191]
[0:12] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x9ffec6]
[0:13] CkDeliverMessageFree+0x21 [0xb2d373]
[0:14] _Z15_processHandlerPvP11CkCoreState+0x70b [0xb2c21b]
[0:15] CsdScheduleForever+0xa5 [0xbf87f3]
[0:16] CsdScheduler+0x1c [0xbf83f4]
[0:17] _ZN7BackEnd7suspendEv+0xb [0x53e3e1]
[0:18] _ZN9ScriptTcl9initcheckEv+0x80 [0xa7c364]
[0:19] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0xa78a94]
[0:20] TclInvokeStringCommand+0x91 [0xc26a58]
[0:21] /home2/emiliawu/NAMD_2.8_Linux-x86_64/namd2 [0xc5c8a8]
[0:22] Tcl_EvalEx+0x176 [0xc5ceeb]
[0:23] Tcl_EvalFile+0x134 [0xc548f4]
[0:24] _ZN9ScriptTcl4loadEPc+0x10 [0xa77e42]
[0:25] _Z18after_backend_initiPPc+0x448 [0x539cc8]
[0:26] main+0x3a [0x53984a]
[0:27] __libc_start_main+0xdb [0x3052d1c3fb]
[0:28] _ZNSt8ios_base4InitD1Ev+0x4a [0x534e3a]
Aborted
On Aug 29, 2011, at 9:36 AM, Giacomo Fiorin wrote:
> Hello Emilia, is there any error or warning message before "Error: no collective variables defined."? There should be.
>
> Please also beware that the way you set up the system you only apply a restraint on the center of mass of the water layer, but individual waters can still diffuse!
>
> For how tedious as this may sound, you need to create two such variables for each water molecule in the system.
>
> On Mon, Aug 29, 2011 at 10:13 AM, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> Hi All,
>
> Sorry for posting this message again, but could anyone give me any suggestion on this, thanks a lot!
>
> I have a question about using colvar to do MD simulation. I am working on a lipid bilayer system, what I am trying to do is restrain the water molecule from going into the hydrophobic core of my system.
> so I used 2 colvar restrain to control the water on the top and the water on the bottom separately. For water with Z coordinate bigger than 0, I tried to keep it in the range of 35 > Z >11, and it works fine. But
> for the water with Z coordinate smaller than 0, I want to keep them in the range of -11 > Z > -35, but it did not work, I copied my colvar file below, and the error message is here. can anyone tell me what's going on here?
> Thanks a lot!
> -------------------------------------------------------------------------------------------
> colvars: Error: no collective variables defined.
> colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Error in the collective variables module: exiting.
> ------------------------------------------------------------------------------------------
>
>
> colvar {
> name waterup
> width 0.1
> lowerboundary 11.0
> upperboundary 35.0
> lowerWall 11.0
> upperWall 35.0
> lowerWallConstant 2.5
> upperWallConstant 2.5
> distanceZ {
> main {
> atomsFile watup_main.ref # use Tcl script to generate this file with selection of all the waters #
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> dummyAtom ( 0.000, 0.000, 0.000 )
> }
> axis (0.0, 0.0, 1.0)
> }
> }
>
>
> colvar {
> name waterdown
> width 0.1
> lowerboundary -35.0
> upperboundary -11.0
> lowerWall -35.0
> upperWall -11.0
> lowerWallConstant 2.5
> upperWallConstant 2.5
> distanceZ {
> main {
> atomsFile watdown_main.ref # use Tcl script to generate this file with selection of all the waters #
> atomsCol B
> atomsColValue 1.0
> }
> ref {
> dummyAtom ( 0.000, 0.000, 0.000 )
> }
> axis (0.0, 0.0, 1.0)
> }
>
>
>
> Emilia
>
>
>
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