Nilesh Dhumal wrote:
Can you tell where I am going worng. Here I pasted my .itp file
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_997 PA 0 100.0000 1.000 A 0.40000e-01 0.82890e-01
opls_998 NE 0 100.0000 -1.000 A 0.40000e-01 0.82890e-01
[ constraints ]
; i j func b0 kb
1 2 1 0.350000
As I said before (and is explained in the manual), [constraints], like any other
bonded parameter, must belong to a [moleculetype], which you have not defined
here. You've got atom types and force field information, but no molecule to
which the constraints are applied.
-Justin
Nilesh
On Tue, July 27, 2010 12:38 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
still I am getting the same error.
Now I added this two lines
[ constraints ]
1 2 1 0.350000
Then you still have the directive in the wrong place.
-Justin
On Tue, July 27, 2010 12:34 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
I am using opls force field. I have solvent.itp file.
I added follwing line in my solvent.itp file.
[ constraints ]
opls_997 opls_998 1 0.350000 I am getting the following error
You don't define constraints with atom types, you use atom numbers.
See
the manual.
Fatal error:
Syntax error - File solvent.itp, line 13
Last line read:
' [ constraints ]'
Invalid order for directive constraints
Then you've put it in the wrong place. Like any other bonded term,
[constraints] belongs to the moleculetype to which the constraint is
to be applied.
-Justin
Nilesh
On Tue, July 27, 2010 11:29 am, Justin A. Lemkul wrote:
Yes, if you define it in a [ constraints ] directive, and use
"constraints =
none" in your .mdp file, so that other bonds will not be converted
to constraints, but the one you explicitly set in the topology
will be used.
-Justin
Nilesh Dhumal wrote:
Can I put constraint on selected bond?
Nilesh
On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote:
1. Using freezegrps is not generally a good idea to fix a
bond length. Look at the constraints mechenism better. Or just
try a bigger force constant in topology.
2. NPT and freezegrps do not interact correctly, since
freezegrps just freezes any changes of atom positions, so they
are not rescaled even if the box size is changed in NPT.
3. Anyway, I think you have defined incorrect groups if your
atoms of interest are still movable. Check a diffusion
constant of your bonded atoms, it should be zero in the case
of freezegrps.
Dr. Vitaly Chaban
I am trying to freeze a bond (3.5 A) in my system. I used
the index file to define group and I added this two lines in
my .mdp file.
freezegrps = PA NE freezedim = Y Y Y Y Y Y
I used g_dist to verify the distance between the freezing
atoms. During the NVT simulation the distace is around 3.449
A and its
constant though out the simulation. For NPT simulation the
distance varies from 3.449 to 3.1. Can you tell why distance
changes in NPT not in NVT. How can I freeze a bond om NPT
simulation?
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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