[gmx-users] Re: question about minimisation

[Mark Abraham]

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

>
> 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
>>
>>
>>
>> --
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>