[gmx-users] pressure scaling more than 1%

[Erik Lindahl]

You system probably isn't equilibrated enough; before you start doing 
any pressure scaling, make sure it runs fine as an NVT ensemble.

The errors you are seeing are caused by the box beginning to oscillate 
(due to huge pressures), and when it gets into a resonance everything 
crashes.

Cheers,

Erik


On Tuesday, Feb 18, 2003, at 21:50 US/Pacific, nanyu101 wrote:

> Dear gmx-users,
>   I have try to make a hole for my ion channel.
> grompp -f run.mdp -o insert.tpr -c dppc.pdb -r dppc.pdb -p dppc.top
> mdrun -v -hole -holep hp.mdp -deffnm insert
>
> But the system told as follows.And I will show you my run.mdp later.
>
> Step 631  Warning: pressure scaling more than 1%, mu: 1.04684 1.04684 
> 1.04684
>
> Step 632  Warning: pressure scaling more than 1%, mu: 104.213 104.213 
> 104.213
>
> Step 633  Warning: pressure scaling more than 1%, mu: 2.66535e+07 
> 2.66535e+07 2.66535e+07
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the 
> x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
>
>
> Pressure Coupling:
>
> title               =  Yo
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  none
> integrator          =  md
> dt                  =  0.001	; ps !
> nsteps              =  5000	; total 10 ps.
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.8
> rcoulomb            =  1.4
> rvdw                =  0.8
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps		    =  DPP	SOL
> tau_t               =  0.1	0.1
> ref_t               =  300	300
> ; Energy monitoring
> energygrps	    =  DPP	SOL
> ; Pressure coupling is not on
> Pcoupl              =  berendsen
> tau_p               =  2.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  no
>
>
> Would anyone give me any suggestions?Thanks very much.
>
> Best wishes,
> Xianhui Wu
> ______________________________________
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