On 7/26/12 6:07 AM, [email protected] wrote:
On 26/07/2012 6:47 PM, [email protected] 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.
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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