[gmx-users] Re: question about minimisation

[Justin Lemkul]

On 7/26/12 6:07 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> On 26/07/2012 6:47 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Ho,
>>> first I minimize my structure. This is the corresponding mdp file:
>>>
>>> define                  = -DPOSRES
>>> integrator              = steep
>>> emtol           = 10
>>> nsteps          = 1500
>>> nstenergy               = 1
>>> energygrps              = System
>>> coulombtype             = PME
>>> rcoulomb                = 0.9
>>> rvdw                    = 0.9
>>> rlist           = 0.9
>>> fourierspacing  = 0.12
>>> pme_order               = 4
>>> ewald_rtol              = 1e-5
>>> pbc                     = xyz
>>>
>>>
>>> and then I run a md run. This is the corresponding mdp file:
>>>
>>> define          = -DPOSRES
>>> integrator              = md
>>> dt                      = 0.001
>>> nsteps          = 5000
>>> nstxout         = 100
>>> nstvout         = 0
>>> nstfout         = 0
>>> nstlog          = 1000
>>> nstxtcout               = 500
>>> nstenergy               = 5
>>> energygrps              = Protein Non-Protein
>>> nstcalcenergy   = 5
>>> nstlist         = 10
>>> ns-type         = Grid
>>> pbc                     = xyz
>>> rlist           = 0.9
>>> coulombtype             = PME
>>> rcoulomb                = 0.9
>>> rvdw            = 0.9
>>> fourierspacing          = 0.12
>>> pme_order               = 4
>>> ewald_rtol              = 1e-5
>>> gen_vel         = yes
>>> gen_temp                = 200.0
>>> gen_seed                = 9999
>>> constraints             = all-bonds
>>> tcoupl          = V-rescale
>>> tc-grps         = Protein  Non-Protein
>>> tau_t           = 0.1      0.1
>>> ref_t           = 298      298
>>> pcoupl          = no
>>>
>>>
>>>
>>> In my topology file I include the restraint files like this:
>>>
>>> ; Include Position restraint file
>>> #ifdef POSRES
>>> #include "posre.itp"
>>> #endif
>>>
>>> #ifdef POSRES
>>> #include "posre_memb.itp"
>>> #endif
>>
>> This won't work for multiple [moleculetype] entries. See
>> http://www.gromacs.org/Documentation/How-tos/Position_Restraints
>>
>>>
>>>
>>> I just recognize that there is a "DPOSRES" in the mdp files and a
>>> "POSRES"
>>> in my topology file. Is this the problem. Do I have to write it the same
>>> way in the several files?
>>
>> http://www.gromacs.org/Documentation/Include_File_Mechanism
>>
>> Mark
>
>
> I just see that the [ position_restraints ] part is included under the
> [dihedral] and not between the [moleculetype] and the [atom] part. And
> according to the site you wrote me this is a problem, right? But this was
> done by gromacs itself. Shell I write it to the [moleculetype] part?
>

A [position_restraints] directive belongs to the [moleculetype] in which it is 
declared.  The original location of the #include statement produced by Gromacs 
is correct; it follows sequentially within the protein [moleculetype].  Your 
inclusion of the membrane restraint file within the protein [moleculetype] is, 
however, incorrect.

> But I can not see why it can not work that I have 2 restriction files? Can
> you please explain it to me?
>

You can have two restraint files for different [moleculetypes] but they must be 
organized as such.

> So you mean that it is indeed important if I call it POSRES oder DPOSRES,
> right?
>

Yes, syntax is crucial.  The proper way to make use of #ifdef blocks is 
described in the manual and in the link Mark posted.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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