On 7/26/12 7:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
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
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.
okey. So the whole thing with [atoms], [bonds], [dihedral] all contains
to
the entry in [moleculetype] , right?
Any directive belongs to the [moleculetype] that immediately precedes it.
Once
a new [moleculetype] is declared (either directly or indirectly via
#include
mechanism), you're working with a different molecule.
But directly before I include the membrane restriction file I include
the
membrane definition:
#include "amber03.ff/dum.itp"
#ifdef POSRES
#include "posre_memb.itp"
#endif
So I thought that it is directly after the atomtype it belongs to. I
thought that it is the same in the case with the water, where first the
water definition is included and after that the restriction of the
water.
Or am I wrong?
Well the #include statement shown here is different than the one you
showed
previously, which was wrong. Please always be sure you're providing
accurate
information - it wastes less time and avoids confusion.
I include the dummy atoms definition right after the ions. Or is this
the
wrong position?
The position of #include statements in this context is irrelevant. You
can list
the [moleculetypes] in any order you like, but the relevant dependent
directives
must be contained appropriately and the order of the listing in
[molecules] must
match the coordinate file. Otherwise, it's fairly flexible.
-Justin
4935 4952 4950 4951 4
4950 4954 4952 4953 4
4954 4973 4972 4974 4
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber03.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/dum.itp"
#ifdef POSRES
#include "posre_memb.itp"
#endif
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.
But when I only use
"define = -POSRES"
instead of
"define = -DPOSRES"
I get the warning:
"WARNING 1 [file mdp file]: Malformed define option -POSRES"
And also at the
"http://www.gromacs.org/Documentation/How-tos/Position_Restraints";
site is written that in the mdp file there has to be
"define = -DPOSRES"
So is this the right way to write it in the mdp file. Although in the
topology file which is generated by pdb2gmx stays "#ifdef POSRES"?
Use of -DPOSRES is correct, for all the above-cited reasons.
-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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