On 26/07/2012 6:47 PM, reising...@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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