[gmx-users] Re: question about minimisation
Justin Lemkul
jalemkul at vt.edu
Thu Jul 26 13:14:19 CEST 2012
On 7/26/12 7:06 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>
>>
>> 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.
>
> okey. So the whole thing with [atoms], [bonds], [dihedral] all contains to
> the entry in [moleculetype] , right?
>
Any directive belongs to the [moleculetype] that immediately precedes it. Once
a new [moleculetype] is declared (either directly or indirectly via #include
mechanism), you're working with a different molecule.
> But directly before I include the membrane restriction file I include the
> membrane definition:
>
> #include "amber03.ff/dum.itp"
> #ifdef POSRES
> #include "posre_memb.itp"
> #endif
>
>
> So I thought that it is directly after the atomtype it belongs to. I
> thought that it is the same in the case with the water, where first the
> water definition is included and after that the restriction of the water.
>
> Or am I wrong?
>
Well the #include statement shown here is different than the one you showed
previously, which was wrong. Please always be sure you're providing accurate
information - it wastes less time and avoids confusion.
> I include the dummy atoms definition right after the ions. Or is this the
> wrong position?
>
The position of #include statements in this context is irrelevant. You can list
the [moleculetypes] in any order you like, but the relevant dependent directives
must be contained appropriately and the order of the listing in [molecules] must
match the coordinate file. Otherwise, it's fairly flexible.
-Justin
>
> 4935 4952 4950 4951 4
> 4950 4954 4952 4953 4
> 4954 4973 4972 4974 4
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "amber03.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "amber03.ff/ions.itp"
>
> #include "amber03.ff/dum.itp"
> #ifdef POSRES
> #include "posre_memb.itp"
> #endif
>
>
>
>
>>
>>> 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
>>
>> --
>> ========================================
>>
>> 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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>
>
--
========================================
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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