[gmx-users] Re: question about minimisation

Thu Jul 26 13:06:26 CEST 2012

>
>
> 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?

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?

I include the dummy atoms definition right after the ions. Or is this the
wrong position?

 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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