Re: [gmx-users] bond, angle and dihedral restraints in Gromacs

[Mark Abraham]

Rebeca García Fandiño wrote:

Thank you very much for the suggestion.
 Actually, I am trying to reproduce the results from another publication 
(JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d 
where they used Gromacs/amber to simulate a CNT. They apply: 
"Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were 
maintained by harmonic potentials with spring constants of 393 960 kJ 
mol^- ^1 nm^- ^2 and 527 kJ mol^- ^1 deg^- ^2 before relaxation. In 
addition, a weak dihedral angle potential was applied to bonded carbon 
atoms.^"


So, as I understand, they apply RESTRAINTS to the bonds, angles and 
dihedrals.


Well, they used potential forms similar to those used in restraints. One 
can use a harmonic "bond" potential (function type 6 IIRC) in GROMACS 
without using a distance restraint. See table 5.4.


I have tried to construct the [distance_restraints] for my system (I 
show you here a little part):


[ distance_restraints ]
; atom1  atom2  type  index  type2  low   up1   up2   fac
1 310 1 1 1 0.142 0.146 0.150 1.0
2 290 1 2 1 0.142 0.146 0.150 1.0
3 291 1 3 1 0.142 0.146 0.150 1.0
(...)

but  I don' t understand very well which value should I write for "low   
up1   up2". The manual says that "the columns low, up1 and up2 hold the 
values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation I 
still don' t understand which should be the better values for my case. I 
have looked into the mail archive, and some other people asked for that, 
but I did not find any proper solution.
How could I choose the best values for "low   up1   up2" to restrain my 
bond values to 1.42 Amstrong?


The other question is about angle restraints, I have found indications 
in the wiki of how to treat the dihedral restraints 
(http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did 
not find any similar for the angle restraints. I have seen in the mail 
archive that 2 pairs of atoms should be used, but I did not find 
anything to trust in. Could you please give me some indications of how 
to treat angle restraints?


Section 4.3.2 and Table 5.5 seem to cover it, I think.

Mark
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Re: [gmx-users] bond, angle and dihedral restraints in Gromacs

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Thank you very much for the suggestion.
 Actually, I am trying to reproduce the results from another publication 
(JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d 
where they used Gromacs/amber to simulate a CNT. They apply: 
"Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were 
maintained by harmonic potentials with spring constants of 393 960 kJ 
mol^- ^1 nm^- ^2 and 527 kJ mol^- ^1 deg^- ^2 before relaxation. In 
addition, a weak dihedral angle potential was applied to bonded carbon 
atoms.^"




A harmonic potential is simply defined as bond type 1 (manual section 4.2.1), 
and similarly for angles (section 4.2.5).  For the bonds, you can specify, i.e.:


[ bonds ]
1   2   1   0.14   393960

Note that Gromacs uses kJ mol^-1 rad^-2 for angle force constants.  The 
information about the dihedrals is vague, so I can't make any suggestion there.


So, as I understand, they apply RESTRAINTS to the bonds, angles and 
dihedrals.


I have tried to construct the [distance_restraints] for my system (I 
show you here a little part):


[ distance_restraints ]
; atom1  atom2  type  index  type2  low   up1   up2   fac
1 310 1 1 1 0.142 0.146 0.150 1.0
2 290 1 2 1 0.142 0.146 0.150 1.0
3 291 1 3 1 0.142 0.146 0.150 1.0
(...)

but  I don' t understand very well which value should I write for "low   
up1   up2". The manual says that "the columns low, up1 and up2 hold the 
values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation I 
still don' t understand which should be the better values for my case. I 
have looked into the mail archive, and some other people asked for that, 
but I did not find any proper solution.
How could I choose the best values for "low   up1   up2" to restrain my 
bond values to 1.42 Amstrong?




These are distances that determine the restoring force to maintain a distance. 
Figure 4.13 is perhaps a bit more illustrative of how they should be 
interpreted, but again I don't believe that you will need distance restraints to 
apply a simple harmonic potential.


-Justin

The other question is about angle restraints, I have found indications 
in the wiki of how to treat the dihedral restraints 
(http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did 
not find any similar for the angle restraints. I have seen in the mail 
archive that 2 pairs of atoms should be used, but I did not find 
anything to trust in. Could you please give me some indications of how 
to treat angle restraints?


Thank you very much,

Best wishes,

Rebeca Garcia
Parc Cientific de Barcelona
Spain







 > Date: Thu, 21 May 2009 12:41:57 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] bond, angle and dihedral restraints in Gromacs
 >
 >
 >
 > Rebeca García Fandiño wrote:
 > > Hello,
 > > I would like to simulate a CNT and I want to apply a harmonic 
potential:

 > > -on the C-C bonds
 > > -on the bond angles
 > > -on the dihedral angles
 > > with a different spring constant for each case.
 > >
 > > I have read Section 4.3 from Gromacs manual, but I actually have some
 > > doubts about how to include this in the topology.
 > >
 > > -for the distance restraints I have tried to use genrestr:
 > >
 > > genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 
40

 > >
 > > The file I obtain is something like:
 > >
 > > ; distance restraints for UNK of cnt_wat_gmx.gro created by
 > > rdparm2gmx.pl Wed May 20 10:20:59 BST 2009
 > >
 > > [ distance_restraints ]
 > > ; i j ? label funct lo up1 up2 weight
 > > 1 2 1 0 1 0.403354 0.603354 1.60335 1
 > > 1 3 1 1 1 0.587676 0.787676 1.78768 1
 > > 1 4 1 2 1 0.769212 0.969212 1.96921 1
 > > 1 5 1 3 1 0.86081 1.06081 2.06081 1
 > > (...)
 > >
 > > This is different from the [distance_restraint] example shown in 
pag 69
 > > of the manual, now I don' t have the fac column. I would like to 
apply a

 >
 > The format of the distance_restraints section appears correct. If you 
read the
 > description of the "fac" column, it is a weighting factor for that 
particular

 > restraint. So therefore, "weight" is probably equivalent.
 >
 > > spring constant of 40 to C-C bonds, but where is the constant 
here?

 > > How could I apply a determined spring constant? In the .mdp file?
 > > Besides, all the distances are restrained... Is there any way to
 > > restrain only the C-C bonds? I mean I don' t want to restrain the
 > > distance between a carbon and a carbon far away from it, only
 > > restraining the neighbouring carbons to a distance of 1.4 A.
 > >
 >
 > You cannot use genrestr for this purpose. Using

RE: [gmx-users] bond, angle and dihedral restraints in Gromacs

[Rebeca García Fandiño]

Thank you very much for the suggestion.
 Actually, I am trying to
reproduce the results from another publication (JACS 2005, 127, 7166)
http://pubs.acs.org/doi/full/10.1021/ja050044d where they used
Gromacs/amber to simulate a CNT. They apply: "Carbon−carbon bond lengths of 
0.14 nm and bond angles of 120° were
maintained by harmonic potentials with spring constants of 393 960 kJ
mol-1 nm-2 and 527 kJ mol-1 deg-2 before relaxation. In addition, a weak 
dihedral angle potential was applied to bonded carbon atoms." 

So, as I understand, they apply RESTRAINTS to the bonds, angles and dihedrals.

I have tried to construct the [distance_restraints] for my system (I show you 
here a little part):

[ distance_restraints ]
; atom1  atom2  type  index  type2  low   up1   up2   fac
1 310 1 1 1 0.142 0.146 0.150 1.0
2 290 1 2 1 0.142 0.146 0.150 1.0
3 291 1 3 1 0.142 0.146 0.150 1.0
(...)

but 
I don' t understand very well which value should I write for "low  
up1   up2". The manual says that "the columns low, up1 and up2 hold the
values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation
I still don' t understand which should be the better values for my
case. I have looked into the mail archive, and some other people asked
for that, but I did not find any proper solution.
How could I choose the best values for "low   up1   up2" to restrain my bond 
values to 1.42 Amstrong?

The
other question is about angle restraints, I have found indications in
the wiki of how to treat the dihedral restraints
(http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did
not find any similar for the angle restraints. I have seen in the mail
archive that 2 pairs of atoms should be used, but I did not find
anything to trust in. Could you please give me some indications of how
to treat angle restraints?

Thank you very much,

Best wishes, 

Rebeca Garcia
Parc Cientific de Barcelona
Spain

> Date: Thu, 21 May 2009 12:41:57 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] bond, angle and dihedral restraints in Gromacs
> 
> 
> 
> Rebeca García Fandiño wrote:
> > Hello,
> > I would like to simulate a CNT and I want to apply a harmonic potential:
> > -on the C-C bonds
> > -on the bond angles
> > -on the dihedral angles
> > with a different spring constant for each case.
> > 
> > I have read Section 4.3 from Gromacs manual, but I actually have some 
> > doubts about how to include this in the topology.
> > 
> > -for the distance restraints I have tried to use genrestr:
> > 
> > genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40
> > 
> >  The file I obtain is something like:
> > 
> > ; distance restraints for UNK of cnt_wat_gmx.gro created by 
> > rdparm2gmx.pl Wed May 20 10:20:59 BST 2009
> > 
> > [ distance_restraints ]
> > ;   i j ? label  funct loup1up2 weight
> > 1 2 1 0  1   0.403354   0.6033541.60335  1
> > 1 3 1 1  1   0.587676   0.7876761.78768  1
> > 1 4 1 2  1   0.769212   0.9692121.96921  1
> > 1 5 1 3  10.860811.060812.06081  1
> > (...)
> > 
> > This is different from the [distance_restraint] example shown in pag 69 
> > of the manual, now I don' t have the fac column. I would like to apply a
> 
> The format of the distance_restraints section appears correct.  If you read 
> the 
> description of the "fac" column, it is a weighting factor for that particular 
> restraint.  So therefore, "weight" is probably equivalent.
> 
> > spring constant of 40 to C-C bonds, but where is the constant here? 
> > How could I apply a determined spring constant? In the .mdp file? 
> > Besides, all the distances are restrained... Is there any way to 
> > restrain only the C-C bonds? I mean I don' t want to restrain the 
> > distance between a carbon and a carbon far away from it, only 
> > restraining the neighbouring carbons to a distance of 1.4 A.
> > 
> 
> You cannot use genrestr for this purpose.  Using genrestr -disre generates a 
> matrix of all atoms you specify.  Also, -fc is expected to be used with 
> position 
> restraints; note the format given in genrestr -h.
> 
> Are you really interested in applying restraints to all bonds, angles, 
> dihedrals, and distances?  Realize that constraints (Section 5.5) and 
> restraints 
> are separate ideas in Gromacs.
> 
> If you want to define your own force constants for bonds, angles, etc. simply 
> do

Re: [gmx-users] bond, angle and dihedral restraints in Gromacs

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Hello,
I would like to simulate a CNT and I want to apply a harmonic potential:
-on the C-C bonds
-on the bond angles
-on the dihedral angles
with a different spring constant for each case.

I have read Section 4.3 from Gromacs manual, but I actually have some 
doubts about how to include this in the topology.


-for the distance restraints I have tried to use genrestr:

genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40

 The file I obtain is something like:

; distance restraints for UNK of cnt_wat_gmx.gro created by 
rdparm2gmx.pl Wed May 20 10:20:59 BST 2009


[ distance_restraints ]
;   i j ? label  funct loup1up2 weight
1 2 1 0  1   0.403354   0.6033541.60335  1
1 3 1 1  1   0.587676   0.7876761.78768  1
1 4 1 2  1   0.769212   0.9692121.96921  1
1 5 1 3  10.860811.060812.06081  1
(...)

This is different from the [distance_restraint] example shown in pag 69 
of the manual, now I don' t have the fac column. I would like to apply a


The format of the distance_restraints section appears correct.  If you read the 
description of the "fac" column, it is a weighting factor for that particular 
restraint.  So therefore, "weight" is probably equivalent.


spring constant of 40 to C-C bonds, but where is the constant here? 
How could I apply a determined spring constant? In the .mdp file? 
Besides, all the distances are restrained... Is there any way to 
restrain only the C-C bonds? I mean I don' t want to restrain the 
distance between a carbon and a carbon far away from it, only 
restraining the neighbouring carbons to a distance of 1.4 A.




You cannot use genrestr for this purpose.  Using genrestr -disre generates a 
matrix of all atoms you specify.  Also, -fc is expected to be used with position 
restraints; note the format given in genrestr -h.


Are you really interested in applying restraints to all bonds, angles, 
dihedrals, and distances?  Realize that constraints (Section 5.5) and restraints 
are separate ideas in Gromacs.


If you want to define your own force constants for bonds, angles, etc. simply do 
so in the topology yourself (Table 5.4).


-Justin

Another question is: Is there any tool to construct the equivalent 
angle_restraints and dihedral_restraints in an authomatic way, or should 
I do it by hand?


Thank you very much in advance for your help.

Best wishes,

Dr. Rebeca Garcia
Parc Cientific de Barcelona
Spain







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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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[gmx-users] bond, angle and dihedral restraints in Gromacs

[Rebeca García Fandiño]

Hello,
I would like to simulate a CNT and I want to apply a harmonic potential:
-on the C-C bonds 
-on the bond angles 
-on the dihedral angles
with a different spring constant for each case.

I have read Section 4.3 from Gromacs manual, but I actually have some doubts 
about how to include this in the topology.

-for the distance restraints I have tried to use genrestr: 

genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 40

 The file I obtain is something like:

; distance restraints for UNK of cnt_wat_gmx.gro created by rdparm2gmx.pl Wed 
May 20 10:20:59 BST 2009

[ distance_restraints ]
;   i j ? label  funct loup1up2 weight
1 2 1 0  1   0.403354   0.6033541.60335  1
1 3 1 1  1   0.587676   0.7876761.78768  1
1 4 1 2  1   0.769212   0.9692121.96921  1
1 5 1 3  10.860811.060812.06081  1
(...)

This is different from the [distance_restraint] example shown in pag 69 of the 
manual, now I don' t have the fac column. I would like to apply a spring 
constant of 40 to C-C bonds, but where is the constant here? How could I 
apply a determined spring constant? In the .mdp file? Besides, all the 
distances are restrained... Is there any way to restrain only the C-C bonds? I 
mean I don' t want to restrain the distance between a carbon and a carbon far 
away from it, only restraining the neighbouring carbons to a distance of 1.4 A.

Another question is: Is there any tool to construct the equivalent 
angle_restraints and dihedral_restraints in an authomatic way, or should I do 
it by hand?

Thank you very much in advance for your help.

Best wishes,

Dr. Rebeca Garcia
Parc Cientific de Barcelona
Spain






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