Nilesh Dhumal wrote:
I am going to put solvent arond this solute. I want to freeze the distance
only for solute not for solvent.
Then the approach I described will work fine. Either constrain all bonds or use
a distance restraint.
-Justin
Nilesl
On Fri, July 30, 2010 10:45 am, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
I put the constraints on PA-NE to keep the bond length 3.5 A.
After calculating the g_dist I noted that the bond length is atound 5.5
A. Can you tell why its taking 5.5 A.
If I difine contraints=all-bonds in mdp file then it shows 3.5 A proper
bond length.
From your original post some time ago, it was not clear that you only had
one bond to deal with. If this is the case, then your approach sounds
fine, just use a normal [ bonds ] directive and set "constraints =
all-bonds." As you say, that works, so I don't see what the problem is.
Are you going to be developing
a more complex system for which you don't want other bonds constrained,
just the one defined below? Another approach would be a distance
restraint, but I don't believe that will absolutely fix the distance,
unless your tolerance is set very strictly.
-Justin
Can u tell where is the problem.
Here I pasted the .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
[ bondtypes ]
; i j func b0 kb
PA NE 1 0.350000 000000
[ moleculetype ]
; name nrexcl
ABC 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 opls_997 1 ABC PA 1 1.0000 100.0000
2 opls_998 1 ABC NE 1 -1.0000 100.000
[ constraints ]
; i j func b0 kb
1 2 1 0.350000
On Tue, July 27, 2010 7:07 pm, Justin A. Lemkul wrote:
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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--
========================================
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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