Re: colvar restrain of water in lipid system

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Aug 29 2011 - 11:17:47 CDT

Hi,

For performance reasons, this kind of restraint is best done in
parallel using TclBC.

Best,
Jerome

On 29 August 2011 16:55, 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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