Re: namd cvs compilation

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Fri Nov 28 2008 - 00:11:14 CST

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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