[gmx-users] Error in pr

[Tsjerk Wassenaar]

Dhananjay,

Consider searching the list archive... All possible solutions are in there.

Cheers,

Tsjerk

On 7/27/07, Dhananjay <dhananjay.c.joshi at gmail.com> wrote:
> Hello all,
>
> I am getting error in pr dynamics when I run mdrun for a protein consist of
> two chains with 326 residues each.
>
> The error is as follows:
>
> Program grompp, VERSION 3.3
> Source code file: readir.c, line: 1131
>
> Fatal error:
> Not enough ref_t and tau_t values!
> -------------------------------------------------------
>
>
>
> I want to perform simulation at 300 K. But how much tau_t value can I vary ?
>
> The mdp file used for the simulation is as follows:
> Can anybody tell me whats wrong here ?
>
>
> Thanking you in advance ........................
>
>
>
> title               =  none
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  500000   ; total 500 ps.
> nstcomm             =  1
> nstxout             =  250
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9      ;nm
> coulombtype         =  PME
> rcoulomb            =  0.9      ;nm
> rvdw                =  1.4
> fourierspacing          =  0.12
> fourier_nx              =  0
> fourier_ny              =  0
> fourier_nz              =  0
> pme_order               =  4
> ewald_rtol              =  1e-5
> optimize_fft            =  yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.5      0.5
> tc_grps             =  protein  sol
> ref_t               =  300      300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  1.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
>
> -- Dhananjay
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623