[gmx-users] protein in water

[Marc Ceruso]

Hi-

Try using  a vdw cut-off of 1.2.
Do you want to restrain something on your system (-DPOSRES)
I would define explicitly the type of coulomb and vdw methods you
want to use, the defaults may change.
Best
marco

________________________________________________________________________________

    Department of Physiology & Biophysics
    Mt Sinai School of Medicine
    One Gustave L. Levy Place
    New York NY 10029

    Tel  : 212-241 82 93
    Fax  : 212-860 33 69
    mceruso at physbio.mssm.edu
________________________________________________________________________________





On Tue, 16 Sep 2003, Dana Reichmann wrote:

> Hi,
>
> I am trying to run simulation of small protein (150 aa) in water. At
> early stages of the  full MD running I got warning:
> " Step 92  Warning: pressure scaling more than 1%, mu: 1.01105 1.01105
> 1.01105"
> The running stopped by error: "Fatal error: ci = -1 should be in 0 ..
> -1 [FILE nsgrid.c, LINE 210]"
>
> Does someone know how should I solve this problem?
>
> Lots of thanks in advance.
> Dana
>
> The mdp file is
>
> title               =  Yo
> cpp                 =  cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000    ; total 20 ps.
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =  Protein  Non-Protein
> tau_t               =  0.1      0.1
> ref_t               =  300      300
> ; Energy monitoring
> energygrps          =  Protein  Non-Protein
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> 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
>
>
>
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