[gmx-users] mdrun_hole problem again ..SOLVED..THANKS.....

[Alok]

Thanks a lot to all of you, especialy Florian and Chris. My problem has been 
solved.

Best regards,
Alok

----- Original Message ----- 
From: <chris.neale at utoronto.ca>
To: <gmx-users at gromacs.org>
Sent: Tuesday, September 05, 2006 4:35 AM
Subject: Re: [gmx-users] mdrun_hole problem again


>- you didn't do an energy minimization
> - you used hz1 0 and I used hz1 1.0
> - you didn't include make hole options hr,hx,hy
>
> *** Somebody already suggested nstlog = 1 and nstenergy = 1, please try 
> that!!!
> In fact make everything 1 (nstxout,nstxtcout,...)
>
> Here is what worked for me with the same POPE file:
>
> 1. Do an energy minimization
>
> 2. run the make_hole mdrun:
>
> grompp -maxwarn 10000 -f grompp_md.mdp -c a.gro -p a.top -o a.tpr
>
> mdrun -nice 4 -hole -holep hole.mdp -s a.tpr -o a.trr -c b.gro -g 
> output.mdrun
> -v -x a.xtc
>
> ############################# em.mdp ############################
>
> title               =  energyMinimization
> cpp                 =  /usr/bin/cpp
> integrator          =  steep
> nsteps              =  500
> emtol               =  200
> emstep              =  0.000005
> comm_mode           =  linear
> nstcomm             =  1
> comm_grps           =  System
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> fourierspacing      =  0.15
> pme_order           =  4
> vdwtype             =  switch
> rvdw_switch         =  0.9
> rvdw                =  1.0
> rlist               =  1.1
> DispCorr            =  no
> Pcoupl              =  no
> tcoupl              =  no
> annealing           =  no
> gen_seed            =  9896
> constraints         =  hbonds
> constraint_algorithm=  shake
> shake_tol           =  0.0001
>
>
> ############################# hole.mdp ############################
>
> holetype                 = Grasp_ascii
> hfm                      = 10
> supf                     = 10
> molsurf_log              = make_hole.log
> hr                       = 0
> hx                       = 0
> hy                       = 0
> hz                       = 3.5
> hp1                      = 1
> hp2                      = 17680
> s1                       = 17681
> s2                       = 43934
> hz1                      = 1.0
> hz2                      = 6.0
> sfm                      = 10.0
> sofs                     = 0
> molsurf_file             = pagpsys_tot_e.surf
> debugsurf                = no
> resforces                = yes
>
> ############################ run.mdp #################################
> title               =  seriousMD
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> integrator          =  md
> nsteps              =  10000
> tinit               =  0
> dt                  =  0.002
> comm_mode           =  None
> nstcomm             =  1
> comm_grps           =  System
> nstxout             =  10000
> nstvout             =  10000
> nstfout             =  10000
> nstlog              =  100
> nstlist             =  10
> nstenergy           =  10000
> nstxtcout           =  250
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  Cut-off
> ;fourierspacing      =  0.15
> ;pme_order           =  4
> vdwtype             =  switch
> rvdw_switch         =  0.9
> rvdw                =  1.1
> rlist               =  1.1
> rcoulomb            =  1.1
> DispCorr            =  no
> Pcoupl              =  Berendsen
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.
> tcoupl              =  nose-hoover
> tc_grps             =  POPE SOL
> tau_t               =  0.05 0.05
> ref_t               =  300. 300.
> annealing           =  no
> gen_vel             =  yes
> gen_temp            =  300.
> gen_seed            =  9896
> constraints         =  hbonds
> constraint_algorithm=  shake
> shake_tol           =  0.0001
>
>
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