[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

[ITHAYARAJA]

On 17 June 2011 10:23, ITHAYARAJA <ithayaraja at gmail.com> wrote:



> Dear Sir,
> Above error was solved but the system has raised a following new error,
> i.e.,
>
> Fatal error:
> 52 atoms are not part of any of the T-Coupling groups
>
> How do I find which atom file has problem?
> help me to solve this problem...........
>
>
>
> My position restraint parameter file is

title               =  cpeptide position restraining
warnings            =  10
cpp                 =  C:\Program Files\CTCBioapps\gromacs3.3\cpp.exe
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  10000    ; total 20.0 ps.
nstcomm             =  1
nstxout             =  250     ;  output coordinates every 0.5 ps
nstvout             =  1000    :  output velocities every 2.0  ps
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype        =  PME
rcoulomb            =  1.0
rvdw                =  1.0
fourierspacing        =  0.12
fourier_nx        =  0
fourier_ny        =  0
fourier_nz        =  0
pme_order        =  6
ewald_rtol        =  1e-5
optimize_fft        =  yes
; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.1    0.1    0.1    0.1    0.1
tc-grps            =  protein  sol    FAD    NDP    GSH
ref_t               =  300      300    300    300    300
; Pressure coupling is not on
Pcoupl              =  no
pcoupltype        =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  310.15
gen_seed            =  173529/n


-- 
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
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