[gmx-users] Re: question about minimisation

[reisingere at rostlab.informatik.tu-muenchen.de]

> 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?

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

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

Thank you

>
>>
>> Thank you
>>
>>
>>> Hi,
>>>
>>> Did you call your genrestr output in your mdp file using define = * ?
>>> (for
>>> example define = -DPOSRES ; where posres was your file name.)
>>>
>>> Thanks
>>>
>>> Peterson J
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://gromacs.5086.n6.nabble.com/question-about-minimisation-tp4999681p4999685.html
>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Only plain text messages are allowed!
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>