[gmx-users] Re: gmx-users Digest, Vol 65, Issue 65

[Nilesh Dhumal]

this is for Energy minimization
title               =  EMI-BF4
cpp                 = /usr/bin/cpp
constraints         =  none
integrator          =  steep
dt                  =  0.002    ; ps !
nsteps              =  50000
nstlist             =  10
coulombtype         = PME
vdwtype             = cut-off
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
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
pbc                 = xyz
;       Energy minimizing stuff
;
emtol               =  1000.0
emstep              =  0.01


this is for Equilibration

title               =  EMI-BF4
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  200000      ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         = PME
vdwtype             = cut-off
rcoulomb            =  1.0
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
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   400
; Pressure coupling is  on
Pcoupl              = parrinello-rahman
pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  400.0
gen_seed            =  173529




On Fri, September 11, 2009 11:27 am, Ragnarok sdf wrote:
>>

>>
>> Ragnarok sdf wrote:
>>
>>> While trying to analyse my several windows with g_wham the following
>>>
>> error
>>> appears :
>>>
>>> Fatal error:
>>> Pull geometry direction not supported
>>>
>>>
>>> my entry files consist on the several px.xvg listed in a .dat entry
>>> file
>> and
>>> the several .tpr from each of the simulations also listed in a
>>> tpr.dat
>> file
>>>
>>
>> Right, but error is coming from the .tpr files, themselves, sort of.
>> Unfortunately g_wham only works when you've specified "pull_geometry =
>> distance" in the .mdp file.  Maybe this should be documented somewhere?
>> g_wham -h does not make this clear.
>>
>> -Justin
>>
>>
>> I could not find it in g_wham -h. So now i only need to change from
>>
> "pull_geometry  = direction" to "pull_geometry = distance"? Is the
> outcome going to be the same? Do I need to include the first simulation in
> the g_wham analysis? By first simulation I mean the one I used to separate
> the dimers and not the ones I have simulated at each starting distance
> obatined from withing the previous one.
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