[gmx-users] thermostats

[Mark Abraham]

On 06/17/2011 03:27 PM, ITHAYARAJA wrote:





Use a descriptive subject line.





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

Get an up-to-date version of GROMACS for much better performance.

> 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

Like I said before, go work out what is missing. How can we tell what 
atoms are missing? Also see the advice here 
http://www.gromacs.org/Documentation/Terminology/Thermostats

Mark

> ; 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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