Re: namd cvs compilation

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Nov 27 2008 - 20:20:46 CST

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.

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