Re: namd cvs compilation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Nov 29 2008 - 06:52:25 CST

Hi Bin,
you should be using 1-2 exclusions, not 1-4, for the RBCG model. This is
likely the cause of your error, as it yields atoms which should have an
exclusion but may be on the order of 20 A apart.
Best,
Peter

BIN ZHANG wrote:
> Hi,
> Yes, I was getting that error.
> About the "Bad global exclusion count", actually, I was running
> a constant volume simulation. I also included my conf file for the
> simulation:
> Also, could you send me an example of conf file for CGMD?
> Thanks a lot.
> Bin
>
>
> ===========================================
> structure ../../common/cg_ionized.psf
> coordinates ../../common/cg_ionized.pdb
> temperature 0
>
> paraTypeCharmm on
> parameters ../../common/rbcg-2007.par
>
> outputEnergies 100
> outputTiming 1000
> restartfreq 1000
> xstFreq 1000
> dcdFreq 1000
> wrapAll on
> wrapNearest on
>
> # 1 fs time step for computation of bonded interactions
> timestep 15
> # 2 fs time step for nonbonded electrostatic and short range vdW
> nonBondedFreq 2
> # 4 fs time step for long range interactions
> fullElectFrequency 4
>
> # Switching function for decay of vdW forces (see Gumbart, Schulten
> paper)
> cutoff 12
>
> stepsPerCycle 20 ;# redo pairlists every twenty steps
>
> cellBasisVector1 110.00 00.00 00.00
> cellBasisVector2 00.00 110.00 00.00
> cellBasisVector3 00.00 00.00 100.00
> cellOrigin 0.00 0.00 -5.00 ;# the *center* of the
> cell
>
> # the z dimension is going to shrink so pad sufficiently
> # the margin could be reduced once the cell is equilibrated
> margin 5
>
> exclude scaled1-4
> 1-4scaling 1.0
>
> cosangles on
>
> langevin on
> langevinDamping 0.5
> langevinTemp 300
> langevinHydrogen no
>
> binaryoutput off
> binaryrestart on
> outputname cg_equil
>
> minimize 2000
> ============================================
>
>
>
> On Nov 27, 2008, at 8:46 PM, Anirban Ghosh wrote:
>
>>
>> Hello Bin,
>>
>> Are you getting the same error for Nxg Nxg Nxg also?
>> If so, the I thin Anton or Peter can answer that one better, because
>> some
>> coefficient values are also associated with these angle parameters.
>>
>> For "Bad global exclusion count", you can try to run a constant volume
>> simulation, that might help.
>>
>>
>> Regards,
>>
>>
>>> Hi, Anirban:
>>> Can I do the same thing for Nxg Nxg Nxg?
>>> Also, I kept getting the error: "FATAL ERROR: Bad global
>>> exclusion count!" while running the CGMD using NAMD CVS version with
>>> "cosangles on".
>>> Does anyone know why this is happening?
>>> I also checked the NAMD troubleshooting page,
>>> (http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
>>>
>>> ), which said "These errors generally indicate that two atoms that are
>>> (ususally implicitly) excluded are on non-neighboring patches or are
>>> more than the cutoff distance apart"
>>> Can anyone explain, at what situation, this will happen?
>>>
>>> Thanks a lot.
>>> Bin
>>>
>>>
>>> On Nov 27, 2008, at 12:27 AM, Anirban Ghosh wrote:
>>>
>>>>
>>>> Hi,
>>>>
>>>> Add the following line to youparameter file, in the section "ANGLES":
>>>>
>>>> Nxg Nxx Nxg 2.988 92
>>>>
>>>> These parameters are pretty much universal for the protein backbone in
>>>> the RBCG model (the angle Nxg Nxx Nxg corresponds to the connection
>>>> glycine-arbitrary amino acid-glycine).
>>>> Or you can use the older .par and .top files successfully.
>>>>
>>>> I was facing the same problem and Anton told me to do this. Hope it
>>>> helps.
>>>>
>>>> Regards,
>>>>
>>>>
>>>>
>>>>
>>>>> Sorry about this, but I think that's the problem.
>>>>> Now I can compile namd, but when I tried to run the CG model, one
>>>>> peculiar
>>>>> error occured:
>>>>>
>>>>> "Unable to find angle parameter for Nxg Nxx Nxg"
>>>>>
>>>>> Is this a reasonable error ?
>>>>>
>>>>> Thanks .
>>>>> Bin
>>>>>
>>>>> On Wed, Nov 26, 2008 at 5:24 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>>>>>
>>>>>> Hi, Axel:
>>>>>>
>>>>>> I just saw your response to the thread "NAMD crashed with
>>>>>> TclForce
>>>>>> turned on"
>>>>>>
>>>>>>> the namd cvs code defines USE_COMPAT_CONST in the headers that
>>>>>>> include tcl.h. defining USE_NON_CONST is incompatible with that
>>>>>>> (see tcl.h). that same should be true for tcl8.4 if you compile
>>>>>>> the cvs. hence my suspicion that you compiled against an
>>>>>>> inconsistent version of the tcl header. this can easily cause
>>>>>>> segfaults regardless of the compiler.
>>>>>>
>>>>>> Does this mean when I try to compile cvs version of NAMD, the
>>>>>> *.tcl
>>>>>> file in the arch folder should no longer use "TCLFLAGS=-DNAMD_TCL
>>>>>> -DUSE_NON_CONST", but instead should be :
>>>>>> "TCLFLAGS=-DNAMD_TCL"?(-DUSE_NON_CONST no longer needed)
>>>>>> Thanks a lot and Happy Thanksgiving.
>>>>>>
>>>>>> Bin
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Nov 26, 2008, at 4:55 PM, BIN ZHANG wrote:
>>>>>>
>>>>>> Hi, all:
>>>>>>> I was trying to build NAMD CVS version(downloaded yesterday) on
>>>>>>> a linux
>>>>>>> cluster, with the arch file:
>>>>>>>
>>>>>>> ==========================================
>>>>>>> NAMD_ARCH = Linux-amd64
>>>>>>> CHARMARCH = mpi-linux-amd64-icc-mpich
>>>>>>> CHARMOPTS = -thread context -memory os
>>>>>>>
>>>>>>> FLOATOPTS = -O3 -fno-rtti -ipo0 -xW -mtune=pentium4
>>>>>>>
>>>>>>> CXX = /opt/mpich/infiniband/intel/bin/mpiCC
>>>>>>> CC = /opt/mpich/infiniband/intel/bin/mpicc
>>>>>>> CXXOPTS = -static-intel $(FLOATOPTS)
>>>>>>> CXXNOALIASOPTS = -fno-alias $(FLOATOPTS)
>>>>>>> COPTS = -static-intel $(FLOATOPTS)
>>>>>>> ==========================================
>>>>>>>
>>>>>>> But it failed with the error:
>>>>>>>
>>>>>>> /usr/include/tcl.h(256): catastrophic error: #error directive:
>>>>>>> define at
>>>>>>> most one of USE_NON_CONST and USE_COMPAT_CONST
>>>>>>> # error define at most one of USE_NON_CONST and
>>>>>>> USE_COMPAT_CONST
>>>>>>> ^
>>>>>>>
>>>>>>> compilation aborted for src/mainfunc.C (code 4)
>>>>>>> make: *** [obj/mainfunc.o] Error 4
>>>>>>>
>>>>>>> Does anyone know what is this error about? How to solve the
>>>>>>> problem
>>>>>>> then?
>>>>>>>
>>>>>>> Thanks a lot and Happy Thanksgiving.
>>>>>>> Bin
>>>>>>>
>>>>>>> PS: the same configuration works for NAMD-2.6
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------------
>>>>>>> The tree of liberty must be refreshed from time to time with the
>>>>>>> blood of
>>>>>>> patriots and tyrants.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------------
>>>>>> The tree of liberty must be refreshed from time to time with the
>>>>>> blood of
>>>>>> patriots and tyrants.
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> --
>>>> Anirban Ghosh
>>>> Grade Based Engineer
>>>> Bioinformatics Team
>>>> Scientific & Engineering Computing Group
>>>> Centre for Development of Advanced Computing
>>>> Pune, India
>>>>
>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------------
>>> The tree of liberty must be refreshed from time to time with the blood
>>> of patriots and tyrants.
>>>
>>
>> --
>> Anirban Ghosh
>> Grade Based Engineer
>> Bioinformatics Team
>> Scientific & Engineering Computing Group
>> Centre for Development of Advanced Computing
>> Pune, India
>>
>>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.

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