[gmx-users] Error in pr

[bmmothan at ucalgary.ca]

hi,

did u specify an index file in your command line for the 2 groups (protein
and SOl?





> 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
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