[gmx-users] Re: question about minimisation
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Thu Jul 26 14:22:48 CEST 2012
Hi okey,
thank you!!
>
>
> On 7/26/12 8:05 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hmm, okey. Thank you.
>> So all in all what I did was correct and it should only minimize the
>> hydrogen atoms and not the rest of the protein nor the membrane. Right?
>>
>
> To sum up:
>
> 1. The Protein-H group does indeed contain only protein heavy atoms.
> 2. Restraints do not guarantee that these atoms will not move, but they
> disfavor
> such motion.
> 3. The initial block of topology you showed us:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> #ifdef POSRES
> #include "posre_memb.itp"
> #endif
>
> was wrong.
>
> 4. The later block of topology:
>
> ; 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
>
> is syntactically correct and likely works as intended.
>
> 5. To invoke position restraints, one needs to prefix with -D, i.e.
> -DPOSRES.
>
> -Justin
>
>>
>>> Quite sure it's just different syntax in topology and mdp file. Compare
>>> to
>>> C;
>>> #define POSRES // expressed as -DPOSRES in the mdp file
>>> #ifdef POSRES // when working in the topology file
>>>
>>> // Linus
>>>
>>> On Thu, Jul 26, 2012 at 1:52 PM,
>>> <reisingere at rostlab.informatik.tu-muenchen.de> wrote:
>>>>>
>>>>>
>>>>> 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
>>>>>>>
>>>>>>> ========================================
>>>>>>> --
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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>>>>
>>>>
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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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