[gmx-users] preprocessing in position restrained step, problem with binary top file

[Justin A. Lemkul]

Moeed wrote:
> I would be most thankful if you could help me warning 1, note 1 and thr 
> fatal error. I I read about -n option but I dont know where in command 
> line i have to include it. Thank you.

Index files are passed to Gromacs tools on the command line, just like all the 
other options.  There is no required order.  I do not believe you need an index 
file; your .mdp file is fundamentally flawed (see below).

As a preface, are we still dealing with your hexane system?  I presume so from 
the names on the grompp command, but it is always best to apprise us of what 
you're doing rather than relying on us to keep track of everyone's problems.

> 
> grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p HexaneModified-Residuename.top -o Hexane_pr >& output.grompp_pr
> 
> 
> output file:
> 
> output.grompp_pr
> 
> 
> *WARNING 1 [file pr.mdp, line unknown]:
>   Unknown or double left-hand 'warnings' in parameter file*
> 

There is no such .mdp option.

> 
> checking input for internal consistency...
> 
> *NOTE 1 [file pr.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.*
> 

There have been numerous list discussions about Berendsen, as well as a good 
body of literature about this topic.  For equilibration and initial relaxation, 
Berendsen is probably fine, but if you need a rigorously-defined canonical 
distribution of kinetic energies, Berendsen is not appropriate.

> Opening library file /chem_soft/gromacs/share/
> gromacs/top/ffoplsaa.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'HEX'

Seems to me like you only have hexane...

> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> 
> NOTE 2 [file HexaneModified-Residuename.top, line unknown]:
>   The largest charge group contains 20 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> 

You've been advised at least twice (if not three times) how to deal with this 
note.  If you want free help, you have to at least demonstrate that you're 
willing to help yourself.  Even if you plow through and manage to get grompp to 
generate your .tpr file, the simulation that it specifies will be deeply flawed, 
if not entirely invalid.

> initialising group options...
> processing index file...
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: readir.c, line: 1007
> 
> *Fatal error:
> Group protein not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' option of grompp.
> In that case use the '-n' option.
> *
> -------------------------------------------------------
> pr.mdp file:*************************************************************
> 
> 
> warnings            =  10
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  500      ; total 1.0 ps.
> nstcomm             =  1
> nstxout             =  10
> 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
> tau_t               =  0.1      0.1
> tc-grps             =  protein  sol
> ref_t               =  300      300

If your system has only hexane, why are you telling grompp that you have a 
protein in water?  I'm guessing you're copying this .mdp file from some 
tutorial.  Before blindly trying to push through, consider what you're doing and 
read the manual.

-Justin

> ; 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
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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