[gmx-users] Re: question about minimisation
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Jul 26 13:52:04 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.
>>>
But when I only use
"define = -POSRES"
instead of
"define = -DPOSRES"
I get the warning:
"WARNING 1 [file mdp file]: Malformed define option -POSRES"
And also at the
"http://www.gromacs.org/Documentation/How-tos/Position_Restraints"
site is written that in the mdp file there has to be
"define = -DPOSRES "
So is this the right way to write it in the mdp file. Although in the
topology file which is generated by pdb2gmx stays "#ifdef POSRES"?
Thank you
>>> -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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