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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