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?
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting! Please don't post (un)subscribe requests
to the list. Use the www interface or send it to
[email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting! Please don't post (un)subscribe requests to
the list. Use the www interface or send it to
[email protected]. Can't
post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting! Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]. Can't
post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
