From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Aug 29 2011 - 11:06:44 CDT
Hi Emilia, I'm not aware of an alternative way.
However, if you're restraining also the lipids, why do you expect water
molecules to get into the bilayer spontaneously?
Giacomo
On Mon, Aug 29, 2011 at 10:55 AM, Ling Wu <emilia.l.wu_at_gmail.com> wrote:
> 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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