[gmx-users] Re: question about minimisation

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

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


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?

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
>