On 7/26/12 8:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hmm, okey. Thank you.
So all in all what I did was correct and it should only minimize the
hydrogen atoms and not the rest of the protein nor the membrane. Right?
To sum up:
1. The Protein-H group does indeed contain only protein heavy atoms.
2. Restraints do not guarantee that these atoms will not move, but they disfavor
such motion.
3. The initial block of topology you showed us:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
#ifdef POSRES
#include "posre_memb.itp"
#endif
was wrong.
4. The later block of topology:
; 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
is syntactically correct and likely works as intended.
5. To invoke position restraints, one needs to prefix with -D, i.e. -DPOSRES.
-Justin
Quite sure it's just different syntax in topology and mdp file. Compare to
C;
#define POSRES // expressed as -DPOSRES in the mdp file
#ifdef POSRES // when working in the topology file
// Linus
On Thu, Jul 26, 2012 at 1:52 PM,
<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"?
Thank you
-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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
