[gmx-users] Dihedral angle in OPLS-AA force field

[alokjain]

Dear All,

I have a basic question on Dihedral angle in OPLS-AA force field.

I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Improper dihedral term.

when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1
version (pdb2gmx option 3) I got following energy terms in my log file.

Energies (kJ/mol)
Bond  Angle   Proper Dih.   Ryckaert-Bell.   LJ-14
1.15231e+03   2.92374e+031.73760e+021.32334e+031.86599e+03
Coulomb-14  LJ (SR)  LJ (LR)  Coulomb (SR)Coulomb (LR)
5.03326e+03  1.39004e+05   -1.66722e+03-9.54632e+05-5.37046e+04
Potential   Kinetic En.   Total Energy   TemperaturePressure (bar)
-8.58528e+05   1.57277e+05   -7.01250e+053.04174e+02   -4.80269e+01

so I am getting two proper dihedral term in output(Proper Dih. and
Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got
following comments

 Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use improper for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), the are
; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment,
; to keep things compatible.

So its mean Proper Dih. which I am getting, In reality it  is Improper
Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if
I am wrong).But in original OPLS force field Improper Dihedral was not
defined so how we can justify uses of Improper Dihedral.


Best regards,
Alok
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Re: [gmx-users] Gromacs version

[Tsjerk Wassenaar]

Hi Raghu,

First of all, if all conditions are equal the two simulations should
be drawn from the same ensemble and should for that reason be
"comparable". However, some routines have changed and we don't really
know whether and how this might influence the ensemble. The best way
to check is to compare simulations. But for that you either need full
convergence or need to have more than one simulation run with each
force field (keeping all other conditions equal).

Best,

Tsjerk

On 9/9/06, Chenyue Xing <[EMAIL PROTECTED]> wrote:

I think the statistical reserves but the two trajectories are not exactly
the same.



On 9/9/06, Ragothaman Yennamalli <[EMAIL PROTECTED]> wrote:
> Dear all,
> I have a query,
> 1. Are two trajectories comparable if each one of them
> has been run in a different version of gromacs? Eg,
> v3.2 and v3.3.
>
> Thanks in advance,
> Regards,
> Raghu
>
> **
> Y. M. Ragothaman,
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Information Technology,
> Jawaharlal Nehru University,
> New Delhi - 110067.
>
> Telephone: 91-11-26717568, 26717585
> Facsimile: 91-11-26717586
> **
>
>
>
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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[gmx-users] constraint distance

[kanin wichapong]

Dear All    I would like to know how to constraint the distance between the different molecule, ex. the ligand and the protein. As far as I know whatever to do the constraint, distance, angle dihedral, it can do just in the same molecule.
    Thank you in advance for all of your help.With Best all regard,Kanin
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Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

[Tsjerk Wassenaar]

Hi Mao-Cai Yan,

A high cosine content usually means you're not in equilibrium, or your
trajectory includes the part in which the system is going to
equilibrium. Now, apparently, you're not interested in equilibrium,
but rather in some event of change, which may be required to go from
the starting structure to the equilibrium state or may be a common
transition in equilibrium (in which case you should definitely observe
it more often before claiming anything regarding equilibrium). A high
cosine content in itself is not a qualitative check for your
simulation or fof the principal components extracted from it. It
merely indicates that you're looking at an event of change of your
system, which can be the relaxation from the starting structure or an
undersampled transition, common to your equilibrium state.

To say anything about equilibrium it would also be better to look at
the RMSD from the time averaged structure obtained at the end of the
simulation, which is a much better indicator than the RMSD from the
starting structure. Note that the number of possible conformations
increases rapidly with increasing RMSD, and you'll find the RMSD level
off well before you have true convergence. For larger systems this may
take 15-25 ns or more!

Hope it helps,

Tsjerk

On 9/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote:

M. Yan wrote:
> Thank you very much.
>
> The significant conformation changes occurred between 3.3ns and 3.9ns,
> which I am interested for. The cosine content in this 0.6ns is low (just
> 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300
> -e 3890"); I want to know whether it indicates that the movement of
> protein IN THIS 0.6ns is believable?
>
>
That depends, since you only see a single event in your 30 ns. It would
be more convincing if you could show that this is reproducible, by doing
multiple simulations with different conditions (e.g. velocities,
temperature, starting structure). If it then happens early on in the
simulations, and they all converge to the same structure as your 30 ns
simulation, then it would be convincing...


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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Re: [gmx-users] constraint distance

[Tsjerk Wassenaar]

Hi Kanin,

The only way to get away with that is to merge your two parts to form
one molecule, with the only connection being a distance_restraint (or
another bonded term if you want to emulate bond-like behaviour such as
a salt-bridge).

Best,

Tsjerk

On 9/11/06, kanin wichapong <[EMAIL PROTECTED]> wrote:

Dear All
I would like to know how to constraint the distance between the
different molecule, ex. the ligand and the protein. As far as I know
whatever to do the constraint, distance, angle dihedral, it can do just in
the same molecule.
Thank you in advance for all of your help.

With Best all regard,
Kanin

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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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[gmx-users] Re: problem with dimer simulation !

[C.W. Liang]

try - cluster, and then as cluster group 
protein.Kay.
hello, Kay
 
thanks so much for your advice, but with -pbc cluster, one of 
the two peptides still move out of the box and frequently jump 
back.
i have no idea about it, any else should i do ?
 
best regards,
 
Liang
 
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[gmx-users] Re: problem with dimer simulation !

[C.W. Liang]

hi cw,using trjconv -pbc nojump should 
remove the jumps. then you can analyse interactions between different 
chains, while it doesn't matter for the analysis where they 
diffuse.daniela
hello, daniela
 
thanks for your reply, it really doesn't matter when i 
calculate the distance between two peptides ?
 
best regards,
 
Liang
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[gmx-users] May I use "-b" and "- e" in the cosine co n tent calculation of PC?

[M. Yan]

Thank you, Tsjerk & David.
Judging from RMSD and other analysis, the system has been in well equilibrium at 5 ns; (however, the cosine contents of last 25 ns and whole 30 ns are also higher than 0.7.) The RMSD during the last 25 nanoseconds (compared to the conformation at 5ns) is within 0.25 nm. After read your letter, I think that the PC1 may be useful, but it cannot represent the global motion of the protein very well because it has not been sampled sufficiently; that is, the significant conformation change observed in PC1 may in fact occur BY ACCIDENT. Did I understand right? 
And do you think it will help if I perform multiple MD simulations to test the reproducibility, just as David suggested? (It is quite time-consuming.)
 
 
Best regards.
 
Mao-Cai Yan
 

 
---Original Message-
Send: 2006-09-11 18:17:16 From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> To:"Discussion list for GROMACS users"  Subject: Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC? 
 
Hi Mao-Cai Yan,
A high cosine content usually means you're not in equilibrium, or yourtrajectory includes the part in which the system is going toequilibrium. Now, apparently, you're not interested in equilibrium,but rather in some event of change, which may be required to go fromthe starting structure to the equilibrium state or may be a commontransition in equilibrium (in which case you should definitely observeit more often before claiming anything regarding equilibrium). A highcosine content in itself is not a qualitative check for yoursimulation or fof the principal components extracted from it. Itmerely indicates that you're looking at an event of change of yoursystem, which can be the relaxation from the starting structure or anundersampled transition, common to your equilibrium state.
To say anything about equilibrium it would also be better to look atthe RMSD from the time averaged structure obtained at the end of thesimulation, which is a much better indicator than the RMSD from thestarting structure. Note that the number of possible conformationsincreases rapidly with increasing RMSD, and you'll find the RMSD leveloff well before you have true convergence. For larger systems this maytake 15-25 ns or more!
Hope it helps,
Tsjerk
On 9/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote:> M. Yan wrote:> > Thank you very much.> >> > The significant conformation changes occurred between 3.3ns and 3.9ns,> > which I am interested for. The cosine content in this 0.6ns is low (just> > 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300> > -e 3890"); I want to know whether it indicates that the movement of> > protein IN THIS 0.6ns is believable?> >> >> That depends, since you only see a single event in your 30 ns. It would> be more convincing if you could show that this is reproducible, by doing> multiple simulations with different conditions (e.g. velocities,> temperature, starting structure). If it then happens early on in the> simulations, and they all converge to the same structure as your 30 ns> simulation, then it would be convincing...>>> --> David.> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,> Dept. of Cell and Molecular Biology, Uppsala University.> Husargatan 3, Box 596,  75124 Uppsala, Sweden> phone:  46 18 471 4205  fax: 46 18 511 755> [EMAIL PROTECTED]    [EMAIL PROTECTED]   http://folding.bmc.uu.se> 
 
 
 
 

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Re: [gmx-users] constrained minimization

[David van der Spoel]

이 선주 wrote:

Dear All

I just saw from the mailing list that David answered that the restrained 
minimization can be done and it is different from the constrained 
minimization. For the torsional parameter optimization, I think I need 
to run minimization after constraining torsion angles. Does anyone know 
the way to constrain the torsion angle during minimization?


this is not implemented I'm afraid. Do you have a reference describing 
how to do it?




Thank you in advance
Sunjoo


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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] genion causing atom to be in multiple T-Coupling groups

[Una Bjarnadottir]

Dear Users,

I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion.  When 
running grompp after genion with the new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  
When looking into the .ndx file atom 33000 is in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  How can I change the group definitions and make sure the groups do not overlap and to be unique? 

It seems to be something wrong with how the genion works for me.  I followed the tutorial and chose the SOL group 
and water molecules were replaced by the Cl ions.  Than I modifyed the 
.top file and took 3 sol molecules and added the 3 ions.


Please help because have not been able to fix the problem with related letters 
on the subject on the list.

Best regards, Una Bjarnadottir


.top before:
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_E   1
Protein_I1
Protein_A  1
SOL 9719

.top after
; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_E   1
Protein_I1
Protein_A  1
SOL 9716
CL-3

These are my commands:
   #
   #Run grompp
   #
   emfile_mdpfile='em.mdp'
   emout='em_out.mdp'
   structure_file='em.tpr'
   os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +water_grofile+ ' -o ' +structure_file+ ' -p ' +topologyfile)


   #
   #Run genion
   #
   ion_out='ion.gro'
   os.system('/usr/local/bin/genion -s '+structure_file+ ' -o ' 
+ion_out+ ' -nname Cl -nn 3')


   #
   #Run grompp
   #
   structure_file_after_genion='em_genion.tpr'
   os.system('/usr/local/bin/grompp -f '+emfile_mdpfile+ ' -po ' 
+emout+ ' -c ' +ion_out+ ' -o ' +structure_file_after_genion+ ' -p ' 
+topologyfile)






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Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups

[David van der Spoel]

Una Bjarnadottir wrote:

Dear Users,

I'm hoping for an answear on my problem with neutralizing my system 
adding 3 Cl ions with genion.  When running grompp after genion with the 
new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  When looking into the .ndx file atom 33000 is 
in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  
How can I change the group definitions and make sure the groups do not 
overlap and to be unique?
It seems to be something wrong with how the genion works for me.  I 
followed the tutorial and chose the SOL group and water molecules were 
replaced by the Cl ions.  Than I modifyed the .top file and took 3 sol 
molecules and added the 3 ions.


Please help because have not been able to fix the problem with related 
letters on the subject on the list.


Best regards, Una Bjarnadottir


What do your tcoupl groups look like?

Could it be System SOL?

The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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SV: Re: [gmx-users] constraint distance

[Soren Enemark]

 Hi,  maybe I am misunderstanding either the manual or the topic.. but - in my world -  I never stop being puzzled by the part of chapt 6 in the manual which apparently  says that such distance constraining is possible even though it (seems) to be  secretly known that it is _not_ possible unless one uses the method suggested  below.  I believe, I suggest adding a comment in the manual.   -SorenTsjerk Wassenaar <[EMAIL PROTECTED]> skrev: Hi Kanin,The only way to get away with that is to merge your two parts to formone molecule, with the only connection being a distance_restraint (oranother bonded term if you want to emulate bond-like behaviour such asa salt-bridge).Best,TsjerkOn 9/11/06, kanin wichapong  wrote:> Dear All> I would like to know how to constraint the distance between the> different molecule, ex. the ligand and the protein. As far as I know> whatever to do the constraint, distance, angle dihedral, it can do just in> the same molecule.> Thank you in advance for all of your help.>> With Best all regard,> Kanin>> ___> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> 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>>-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical
 ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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___
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Re: SV: Re: [gmx-users] constraint distance

[David van der Spoel]

Soren Enemark wrote:

 Hi,
 maybe I am misunderstanding either the manual or the topic.. but - in 
my world -
 I never stop being puzzled by the part of chapt 6 in the manual which 
apparently
 says that such distance constraining is possible even though it (seems) 
to be
 secretly known that it is _not_ possible unless one uses the method 
suggested

 below.
 I believe, I suggest adding a comment in the manual.



can you be more specific which part of the manual you mean?


 -Soren

*/Tsjerk Wassenaar <[EMAIL PROTECTED]>/* skrev:

Hi Kanin,

The only way to get away with that is to merge your two parts to form
one molecule, with the only connection being a distance_restraint (or
another bonded term if you want to emulate bond-like behaviour such as
a salt-bridge).

Best,

Tsjerk

On 9/11/06, kanin wichapong wrote:
 > Dear All
 > I would like to know how to constraint the distance between the
 > different molecule, ex. the ligand and the protein. As far as I know
 > whatever to do the constraint, distance, angle dihedral, it can
do just in
 > the same molecule.
 > Thank you in advance for all of your help.
 >
 > With Best all regard,
 > Kanin
 >
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 > www interface or send it to [EMAIL PROTECTED]
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 > http://www.gromacs.org/mailing_lists/users.php
 >
 >


-- 


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Re: problem with dimer simulation !

[David van der Spoel]

C.W. Liang wrote:

try - cluster, and then as cluster group protein.
Kay.
hello, Kay
 
thanks so much for your advice, but with -pbc cluster, one of the two 
peptides still move out of the box and frequently jump back.

i have no idea about it, any else should i do ?
 


merge the peptides into one protein (pdb2gmx -merge) and make a distance 
restraint between them with distance much larger than the actual 
distance. you only need to do this for post-processing the output, not 
for the simulation.




best regards,
 
Liang
 





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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: SV: Re: [gmx-users] constraint distance

[Mark Abraham]

>  Hi,
>   maybe I am misunderstanding either the manual or the topic.. but - in my
> world -
>   I never stop being puzzled by the part of chapt 6 in the manual which
> apparently
>   says that such distance constraining is possible even though it (seems)
> to be
>   secretly known that it is _not_ possible unless one uses the method
> suggested
>   below.
>   I believe, I suggest adding a comment in the manual.

I agree that a comment in the restrains section of Chapter 4 would be in
order. The truth that you can only use restraints between atoms of the
same molecule is clearly implied by Table 5.4, but that's a bit oblique.

Mark

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Re: [gmx-users] Dihedral angle in OPLS-AA force field

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Dear All,

I have a basic question on Dihedral angle in OPLS-AA force field.

I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Improper dihedral term.

when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1
version (pdb2gmx option 3) I got following energy terms in my log file.

Energies (kJ/mol)
Bond  Angle   Proper Dih.   Ryckaert-Bell.   LJ-14
1.15231e+03   2.92374e+031.73760e+021.32334e+031.86599e+03
Coulomb-14  LJ (SR)  LJ (LR)  Coulomb (SR)Coulomb (LR)
5.03326e+03  1.39004e+05   -1.66722e+03-9.54632e+05-5.37046e+04
Potential   Kinetic En.   Total Energy   TemperaturePressure (bar)
-8.58528e+05   1.57277e+05   -7.01250e+053.04174e+02   -4.80269e+01

so I am getting two proper dihedral term in output(Proper Dih. and
Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got
following comments

 Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use improper for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), the are
; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment,
; to keep things compatible.

So its mean Proper Dih. which I am getting, In reality it  is Improper
Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if
I am wrong).But in original OPLS force field Improper Dihedral was not
defined so how we can justify uses of Improper Dihedral.



yes that's correct. AFAIK improper dihedrals are used in OPLS for 
instance for keeping rings flat.



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups

[Mark Abraham]

> Dear Users,
>
> I'm hoping for an answear on my problem with neutralizing my system
adding
> 3 Cl ions with genion.  When
> running grompp after genion with the new generated .gro file I get this
error:
>
> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

Read closely - "T-Coupling group", not "group". You choose the T-Coupling
groups from among those in the .ndx file (or from the default groups in
its absence, as you're doing here) and specify them in the .mdp file. Thus
you should look there first of all. You need to use a disjoint set of
T-Coupling groups, so this error is consistent with not having done that.
If you were using .ndx file (which you aren't), it might be possible your
.ndx file doesn't correspond to your post-genion structure and something
weird happens. I'd expect GROMACS woud die with a more helpful error in
such a case though.

Mark




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Re: [gmx-users] Dihedral angle in OPLS-AA force field

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Dear All,

I have a basic question on Dihedral angle in OPLS-AA force field.

I read some of the papers related to development of OPLS force field where
they have different formula for calculating the torsion angle
I think that is Ryckaert-Bellemans function, but there is no separate term
for Improper dihedral term.

when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1
version (pdb2gmx option 3) I got following energy terms in my log file.

Energies (kJ/mol)
Bond  Angle   Proper Dih.   Ryckaert-Bell.   LJ-14
1.15231e+03   2.92374e+031.73760e+021.32334e+031.86599e+03
Coulomb-14  LJ (SR)  LJ (LR)  Coulomb (SR)Coulomb (LR)
5.03326e+03  1.39004e+05   -1.66722e+03-9.54632e+05-5.37046e+04
Potential   Kinetic En.   Total Energy   TemperaturePressure (bar)
-8.58528e+05   1.57277e+05   -7.01250e+053.04174e+02   -4.80269e+01

so I am getting two proper dihedral term in output(Proper Dih. and
Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got
following comments

 Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use improper for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), the are
; actually implemented as proper dihedrals [1+cos(2*x+180)] for the moment,
; to keep things compatible.

So its mean Proper Dih. which I am getting, In reality it  is Improper
Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if
I am wrong).But in original OPLS force field Improper Dihedral was not
defined so how we can justify uses of Improper Dihedral.



yes that's correct. AFAIK proper dihedrals are used in OPLS for instance 
for keeping rings flat.



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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SV: Re: SV: Re: [gmx-users] constraint distance

[Soren Enemark]

David van der Spoel <[EMAIL PROTECTED]> skrev: Soren Enemark wrote:>  Hi,>  maybe I am misunderstanding either the manual or the topic.. but - in > my world ->  I never stop being puzzled by the part of chapt 6 in the manual which > apparently>  says that such distance constraining is possible even though it (seems) > to be>  secretly known that it is _not_ possible unless one uses the method > suggested>  below.>  I believe, I suggest adding a comment in the manual.> can you be more specific which part of the manual you mean? Basically almost anywhere in chapter 6 from 6.1 to 6.25 included.I mean, pulling works between 2 different molecules, why is it then obvious that constraining doesn't?   > 
 -Soren> > */Tsjerk Wassenaar /* skrev:> > Hi Kanin,> > The only way to get away with that is to merge your two parts to form> one molecule, with the only connection being a distance_restraint (or> another bonded term if you want to emulate bond-like behaviour such as> a salt-bridge).> > Best,> > Tsjerk> > On 9/11/06, kanin wichapong wrote:>  > Dear All>  > I would like to know how to constraint the distance between the>  > different molecule, ex. the ligand and the protein. As far as I know>  > whatever to do the constraint, distance, angle dihedral, it can> do just in>  > the same molecule.>  > Thank you in advance for all of your help.>  >>  > With Best all regard,>  >
 Kanin>  >>  > ___>  > gmx-users mailing list gmx-users@gromacs.org>  > http://www.gromacs.org/mailman/listinfo/gmx-users>  > 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>  >>  >> > > -- > > Tsjerk A. Wassenaar, M.Sc.> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)> Dept. of Biophysical Chemistry> University of Groningen> Nijenborgh 4> 9747AG Groningen, The Netherlands> +31 50 363 4336> ___> gmx-users mailing list gmx-users@gromacs.org>
 http://www.gromacs.org/mailman/listinfo/gmx-users> 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> > > > > > ___> gmx-users mailing listgmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> 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-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala
 University.Husargatan 3, Box 596,   75124 Uppsala, Swedenphone: 46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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___
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[gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

[Una Bjarnadottir]

Una Bjarnadottir wrote:


Dear Users,

I'm hoping for an answear on my problem with neutralizing my system 
adding 3 Cl ions with genion.  When running grompp after genion with the 
new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  When looking into the .ndx file atom 33000 is 
in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  
How can I change the group definitions and make sure the groups do not 
overlap and to be unique?
It seems to be something wrong with how the genion works for me.  I 
followed the tutorial and chose the SOL group and water molecules were 
replaced by the Cl ions.  Than I modifyed the .top file and took 3 sol 
molecules and added the 3 ions.


Please help because have not been able to fix the problem with related 
letters on the subject on the list.


Best regards, Una Bjarnadottir

 


What do your tcoupl groups look like?


tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER otherwise error


Could it be System SOL?


The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.


I made the indes file after running genion using the .gro output file from genion generating it.  Also I thought you would have to subtract one and it was groups 14 and 0 instead of 15 and 1.  How would I have the ions part of the solvent T coupling group?  By modifying the .top file to 
[ molecules ]

; Compound#mols
Protein_E   1
Protein_I   1
Protein_A   1
SOL+CL-  9719

and than the tc-grps in the .mdp file accordingly to that.  How will I define SOL and CL- together, I tryed 
SOL+CL- and SOL-CL- but Fatal error: No such moleculetype SOL+CL- came for both. 

Best regards David for your reply, Una 
David.


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[gmx-users] RE: gmx-users Digest, Vol 29, Issue 23

[Copps, Jeffrey]

Title: RE: gmx-users Digest, Vol 29, Issue 23







Message: 6
Date: Sun, 10 Sep 2006 18:02:50 -0700
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] TFE .gro files
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Copps, Jeffrey wrote:
>
>  Hello all,
>
>  Does anyone have TFE (trifluoroethanol) .gro files that they might
> be willing to share?  Or, barring that, can anyone tell me how to create
> a solvent .gro file?
>
>  Much thanks,
>
>  Jeff Copps
>
>
> 
>
> ___
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how about the united atom one in the share/gromacs/top directory?
otherwise, use prodrg followed by genconf and pressure coupled MD.

--
David.

Unfortunately, unless it's under some unintuitive filename, it's missing from my share/top directory.

Jeff




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Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

[David van der Spoel]

Una Bjarnadottir wrote:

Una Bjarnadottir wrote:


Dear Users,

I'm hoping for an answear on my problem with neutralizing my system 
adding 3 Cl ions with genion.  When running grompp after genion with 
the new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 
and 1 are Cl and protein groups if I on the other hand do not 
neutralize the system the run goes fine!  When looking into the .ndx 
file atom 33000 is in 4 groups;  0 (system), 11 (non-protein), 14 
(SOL) and 16 (other).  How can I change the group definitions and 
make sure the groups do not overlap and to be unique?
It seems to be something wrong with how the genion works for me.  I 
followed the tutorial and chose the SOL group and water molecules 
were replaced by the Cl ions.  Than I modifyed the .top file and took 
3 sol molecules and added the 3 ions.


Please help because have not been able to fix the problem with 
related letters on the subject on the list.


Best regards, Una Bjarnadottir

 


What do your tcoupl groups look like?


tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER 
otherwise error



Could it be System SOL?


The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.


I made the indes file after running genion using the .gro output file 
from genion generating it.  Also I thought you would have to subtract 
one and it was groups 14 and 0 instead of 15 and 1.  How would I have 
the ions part of the solvent T coupling group?  By modifying the .top 
file to [ molecules ]

; Compound#mols
Protein_E   1
Protein_I   1
Protein_A   1
SOL+CL-  9719

and than the tc-grps in the .mdp file accordingly to that.  How will I 
define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal 
error: No such moleculetype SOL+CL- came for both.

Best regards David for your reply, Una David.


in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and 
15 is CL-)




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] RE: gmx-users Digest, Vol 29, Issue 23

[David van der Spoel]

Copps, Jeffrey wrote:


Message: 6
Date: Sun, 10 Sep 2006 18:02:50 -0700
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] TFE .gro files
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Copps, Jeffrey wrote:
 >
 >  Hello all,
 >
 >  Does anyone have TFE (trifluoroethanol) .gro files that they might
 > be willing to share?  Or, barring that, can anyone tell me how to create
 > a solvent .gro file?
 >
 >  Much thanks,
 >
 >  Jeff Copps
 >
 >
 > 
 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org
 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > 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
how about the united atom one in the share/gromacs/top directory?
otherwise, use prodrg followed by genconf and pressure coupled MD.

--
David.

Unfortunately, unless it's under some unintuitive filename, it's missing 
from my share/top directory.





sorry can't find it anymore..

then you'll have to go the second route.


Jeff




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Free energy, frozen atoms and exclusions

[Ignacio Fernández Galván]

Hi all,

I'm trying to calculate solvation free energies and I've found
something "strange".

The thing is I'm interested in free energy of rigid molecules (I
consider other contributions separately), typically a small solute
molecule in water. I'm making a test with methanol. The setup is a
frozen methanol molecule in a box of of water molecules. Since I'm
considering rigid molecules, I create an .itp file with no bonded
terms, just atoms (with charges and LJ). The methanol molecule is
called MOH, and I have this in the .mdp:

energy_grps  = MOH
energygrp_excl   = MOH MOH
freezegrps   = MOH
freezedim= y y y

which should freeze the methanol and disregard all nonbonded terms
between the methanol atoms (and there are no bonded terms).

Well, after the usual equilibration and such, I get this output for the
initial configuration with lambda=1:

LJ (SR): 5.70341e+03
Coulomb (SR): -3.65377e+04
...
dVpot/dlambda: 2.81161e+02

It seems right, but after simulation for several lambda values I get a
free energy of around 10 times what I would expect.

Now I repeat exactly the same simulation, but adding all pairs of
methanol atoms in the [exclusions] of the .itp file. For the same
initial configuration as before, I get this:

LJ (SR): 5.70341e+03
Coulomb (SR): -3.65377e+04
...
dVpot/dlambda: 2.14385e+00

(the only difference is in dVpot/dlambda). This (if I extrapolate)
would give a much more sensible value for the free energy.

As far as I could understand, having "energygrp_excl = MOH MOH" should
be the same as putting all atoms in the [exclusions] section, but it
obviously isn't, at least when it comes to calculating dVpot/dlambda.

Is there something I'm missing? A bug/feature in the code? A
limitation?

Thanks in advance

PS. As a side question, I'd say that, if I have a frozen molecule it
would be best *not* to remove the center of mass motion (not even of
the rest of the system). Am I right?



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RE: [gmx-users] Free energy, frozen atoms and exclusions

[Berk Hess]

From: Ignacio Fernández Galván <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users 
To: gmx-users@gromacs.org
Subject: [gmx-users] Free energy, frozen atoms and exclusions
Date: Mon, 11 Sep 2006 15:18:01 +0100 (BST)

Hi all,

I'm trying to calculate solvation free energies and I've found
something "strange".

The thing is I'm interested in free energy of rigid molecules (I
consider other contributions separately), typically a small solute
molecule in water. I'm making a test with methanol. The setup is a
frozen methanol molecule in a box of of water molecules. Since I'm
considering rigid molecules, I create an .itp file with no bonded
terms, just atoms (with charges and LJ). The methanol molecule is
called MOH, and I have this in the .mdp:

energy_grps  = MOH
energygrp_excl   = MOH MOH
freezegrps   = MOH
freezedim= y y y

which should freeze the methanol and disregard all nonbonded terms
between the methanol atoms (and there are no bonded terms).

Well, after the usual equilibration and such, I get this output for the
initial configuration with lambda=1:

LJ (SR): 5.70341e+03
Coulomb (SR): -3.65377e+04
...
dVpot/dlambda: 2.81161e+02

It seems right, but after simulation for several lambda values I get a
free energy of around 10 times what I would expect.

Now I repeat exactly the same simulation, but adding all pairs of
methanol atoms in the [exclusions] of the .itp file. For the same
initial configuration as before, I get this:

LJ (SR): 5.70341e+03
Coulomb (SR): -3.65377e+04
...
dVpot/dlambda: 2.14385e+00

(the only difference is in dVpot/dlambda). This (if I extrapolate)
would give a much more sensible value for the free energy.

As far as I could understand, having "energygrp_excl = MOH MOH" should
be the same as putting all atoms in the [exclusions] section, but it
obviously isn't, at least when it comes to calculating dVpot/dlambda.

Is there something I'm missing? A bug/feature in the code? A
limitation?


If you are using PME, the mesh contribution is not excluded when
using energygrp_excl, grompp should give you a warning about this.
Adding all the pairs as exclusions solves this problem.



Thanks in advance

PS. As a side question, I'd say that, if I have a frozen molecule it
would be best *not* to remove the center of mass motion (not even of
the rest of the system). Am I right?


Yes.
Note that there are still issues with freeze-groups and pressure scaling
as the rest of the system scales around your frozen atoms.
There is currently no solution for this,
although slow coupling would help.

But why do you want to freeze the methonal?
Things would be much easier with a free methanol.

Berk.


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RE: [gmx-users] Free energy, frozen atoms and exclusions

[Ignacio Fernández Galván]

--- Berk Hess <[EMAIL PROTECTED]> wrote:

> >Is there something I'm missing? A bug/feature in the code? A
> >limitation?
> 
> If you are using PME, the mesh contribution is not excluded when
> using energygrp_excl, grompp should give you a warning about this.
> Adding all the pairs as exclusions solves this problem.

Thanks. Would that account for such a large difference, considering
it's a neutral molecule (and at lambda=1, with no partial charges)?

Well... since it's the derivative, and that means the free energy
change from lambda=0 to lambda=1... yes that could be it. Is this
mentioned in the manual? 'Cause I read about the [exclusions] section
and it gives the advice to use energygrp_excl, but doesn't warn about
this.

Would normal Ewald or reaction field work as (I) expected? I guess I
will keep using PME anyway, if it's as easy as adding the [exclusions].

> But why do you want to freeze the methonal?
> Things would be much easier with a free methanol.

At the moment this is only a test. I need the method to work for
arbitrary molecules for which there are no force field parameters, only
LJ. The atomic charges and intramolecular contributions I get them from
other QM/MM calculations. I also need to compare with other rigid-body
simulations. I'm not saying this is the best way to calculate free
energies, but it's the way I need now :)

Thanks a lot for the reply!

PS. The manual mentions using "no" for "comm_mode", but grompp prefers
"none" instead.



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[gmx-users] constraint distance between ligand and protein

[kanin wichapong]

Hi All,    I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protein, i can't merge together because there is no libraly for the ligand force field and then it can't generate the .itp or .top file 
Best RegardKanin    
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[gmx-users] File input/output error: Can not determine precision of trn file

[Bob Johnson]

Hello everyone,
It seems that one of my trajectory files has an error. I get the following
message when using trjconv -f trajectory.trr.

File input/output error: Can not determine precision of trn file

I noticed that there was a previous question about this error message. However,
the only available workaround pertained to trajectories saved in xtc format.
Has there be any new developments for the trr format?
Thanks,
Bob
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[gmx-users] Re: constrained minimization (David van der Spoel)

[이 선주]

> Dear All
>
> I just saw from the mailing list that David answered that the 

restrained

> minimization can be done and it is different from the constrained
> minimization. For the torsional parameter optimization, I think I need
> to run minimization after constraining torsion angles. Does anyone know
> the way to constrain the torsion angle during minimization?
>
this is not implemented I'm afraid. Do you have a reference describing
how to do it?



I am afraid not...


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[gmx-users] OPLS-AA force field again regarding 1-4 interaction

[alokjain]

Thanks David for your reply, I have a another doubt on OPLS force field
regarding 1-4 interaction.

In manual (chapter 4 page no 62) it was written The use of RB potential
implies exclusion of LJ interaction between first and the last atom of the
dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14
energy in my log file (see below) is there is any problem in this
simulation or it is normal?

Energies (kJ/mol)
Bond   Angle Proper Dih.Ryckaert-Bell.   LJ-14
1.15231e+03   2.92374e+031.73760e+021.32334e+031.86599e+03
Coulomb-14 LJ (SR) LJ (LR)  Coulomb (SR)Coulomb (LR)
5.03326e+03  1.39004e+05-1.66722e+03-9.54632e+05-5.37046e+04
Potential   Kinetic En.   Total Energy   TemperaturePressure (bar)
-8.58528e+05   1.57277e+05   -7.01250e+053.04174e+02   -4.80269e+01

and what I understood from articles on OPLS force field that it scale down
the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in
ffoplsaa.itp file

; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   3   yes 0.5 0.5

what about GROMOS96 force field, it is mention in manual (Chapter 4 page
no 75) it also scale down the LJ-14 repulsion term .
what I understood by manual that It uses separate parameter for LJ-14
interaction Is it is correct? If yes then It uses separate parameters only
for LJ repulsive term or all the non bonded terms i.e.  LJ repulsive,LJ
attractive and for coulomb term?

Best regards,
Alok









> [EMAIL PROTECTED] wrote:
>> Dear All,
>>
>> I have a basic question on Dihedral angle in OPLS-AA force field.
>>
>> I read some of the papers related to development of OPLS force field
>> where
>> they have different formula for calculating the torsion angle
>> I think that is Ryckaert-Bellemans function, but there is no separate
>> term
>> for Improper dihedral term.
>>
>> when I tried to run a simulation using OPLS-AA force field gromacs 3.2.1
>> version (pdb2gmx option 3) I got following energy terms in my log file.
>>
>> Energies (kJ/mol)
>> Bond  Angle   Proper Dih.   Ryckaert-Bell.   LJ-14
>> 1.15231e+03   2.92374e+031.73760e+021.32334e+031.86599e+03
>> Coulomb-14  LJ (SR)  LJ (LR)  Coulomb (SR)Coulomb (LR)
>> 5.03326e+03  1.39004e+05   -1.66722e+03-9.54632e+05-5.37046e+04
>> Potential   Kinetic En.   Total Energy   TemperaturePressure
>> (bar)
>> -8.58528e+05   1.57277e+05   -7.01250e+053.04174e+02   -4.80269e+01
>>
>> so I am getting two proper dihedral term in output(Proper Dih. and
>> Ryckaert-Bell.).But when I checked the ffoplsaabon.itp file I got
>> following comments
>>
>>  Improper OPLS dihedrals to keep groups planar.
>> ; (OPLS doesnt use improper for chiral atoms).
>> ; Since these functions are periodic of the form 1-cos(2*x), the are
>> ; actually implemented as proper dihedrals [1+cos(2*x+180)] for the
>> moment,
>> ; to keep things compatible.
>>
>> So its mean Proper Dih. which I am getting, In reality it  is Improper
>> Dihedral? and Ryckaert-Bell for proper dihedral, (please correct me if
>> I am wrong).But in original OPLS force field Improper Dihedral was not
>> defined so how we can justify uses of Improper Dihedral.
>>
>
> yes that's correct. AFAIK proper dihedrals are used in OPLS for instance
> for keeping rings flat.
>
>
> --
> David.
> 
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
> 
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[gmx-users] Re: Gromacs-CPMD: QMMM

[Pradip Kumar Biswas]

Hi Amit,

Please open epot.inc in SOURCE folder of CPMD-3.11.1, search for MAXNEAR and  change the statement:

PARAMETER (MAXNEAR=2000)

to

PARAMETER (MAXNEAR=5000)

best,
pb.


On Sep 11, 2006, at 3:52 PM, [EMAIL PROTECTED] wrote:

Dear Dr. Biswas,
I am getting following error while running gromacs-cpmd interface for my
system.

LMAX-OF-MMQ-EXP0
INTML-UPD-FREQ10
OUTRL-UPD-FREQ50
MM-Near 4289
INTERFACE| Error: MAXNEAR not big enough!
Increase this value in epot.inc


PROGRAM STOPS IN SUBROUTINE INTERFACE| To many near atoms. [PROC=   0]


with regards,
amit


--
Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
http://comppsi.csuohio.edu/groups/people/biswas.html 
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[gmx-users] unsubscribe

[JMiranda]

[EMAIL PROTECTED] 

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of [EMAIL PROTECTED]
Sent: sexta-feira, 8 de Setembro de 2006 2:46
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Simulation problem with extended membrane system!

Having actually looked back at my notes, here is what I did to extend
pope.pdb into a larger system. However, the suggestion that I posted last
time should work just as well.

1. Remove all waters
2. Duplicate the box until your heart's content. Make it larger than you
actually want because the box will collapse to some extent.
3. MD with Z-only posre on lipid head groups (X and Y force components =
zero). 
This step must be done with constant pressure (In this procedure, make sure
to use isotropic pressure coupling so that the box max and min z don't come
into contact with the membrane).

NOTE for step 3: It is assumed that your edges line up with each other. Load
the system into vmd and show periodic unit cells to make sure. If they line
up poorly then I would find a new starting PDB. However, pope.pdb lines up
well.

4. Adjust the z-dimension to what you want it to be, center your membrane in
the z if you want to.
5. solvate the system.
6. Remove any waters that were placed within the membrane 7. energy minimize
8. posre run as before to allow the water to adjust to the membrane
surfaces. 
However, during this run (and all the rest of the steps) I use semiisotropic
Pcoupling.
9. equilibration phase without any position restraints 10. production run.

If you are going to add protein, you could do that with the results of step
4 since most procedures involve stripping out any waters anyway.

Again, the procedure that I outlined previously should work, but I have not
tested that procedure, only this one.
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[gmx-users] Re: Simulation problem with extended membrane system!

[chris . neale]

I just remembered that I previously posted a script to assist in removing waters
based on their z position:

http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html


>Back to the previous question, after solvate the lipids in water, can I
>remove the water placed in the membrane with excel instead of script? Cause
>with editconf we can know the z dimension of the lipids_only system, let's
>say 6, so if I center the whole system with 0 0 0, the water molecules with
>z coordinates below 3 and above -3 will be excluded. If I'm right, I think
>excel can do it too, or the scripts have some advantages?
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[gmx-users] problem about "order parameter"

[clark]

I am performing some simulation about common protein.I am puzzled when I want to get the order parameter(S2, N-H bond in main chian) to compare with the result of my NMR experiment.Who can give me a detailed way to get this parameter in Gromacs3.3.1? Thanks ! 

   
  
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Re: [gmx-users] problem about "order parameter"

[David van der Spoel]

clark wrote:
I am performing some simulation about common protein.I am puzzled when I 
want to get the order parameter(S2, N-H bond in main chian) to compare 
with the result of my NMR experiment.


Who can give me a detailed way to get this parameter in Gromacs3.3.1?

Thanks !




g_rotacf

you need very long simulations for this to converge.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] changing the parameter numbers for torsion

[Rongliang Wu]

hello,gmx-users

i have a force field that contain 7 rychaert-bellemans dihedral 
coefficients, but in gromacs there are only 6, how can i manage it ?
and where i should change the source code?

regards!

thanks!


Rongliang Wu
[EMAIL PROTECTED]
　　2006-09-12
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Re: [gmx-users] changing the parameter numbers for torsion

[David van der Spoel]

Rongliang Wu wrote:

hello,gmx-users

i have a force field that contain 7 rychaert-bellemans dihedral 
coefficients, but in gromacs there are only 6, how can i manage it ?
and where i should change the source code?

maybe you can combine a RB with a proper dihedral with n=7 over the same 
bond.



regards!

thanks!


Rongliang Wu
[EMAIL PROTECTED]
　　2006-09-12




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] re: non-bonded interactions in GROMACS

[chris . neale]

>In manual (chapter 4 page no 62) it was written The use of RB potential 
>implies exclusion of LJ interaction between first and the last atom of the 
>dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 
>energy in my log file (see below) is there is any problem in this 
>simulation or it is normal? 

Only the 1-4 interactions spanning RB potentials should be excluded from LJ-14 
and coulomb-14. For example, lipid headgroups may be treated without RB's and 
the acyl chains treated with RB's. If you want to see where things are coming 
from, make an index file and then use enerygrps in your .mdp so that g_energy 
can give you some useful output for further testing. Look at your [ pairs ] 
section in your .itp file. Those are the source of the LJ-14 and Coulomb-14 
energies.

>and what I understood from articles on OPLS force field that it scale down 
>the LJ-14 and Coulomb-14 energy my a factor of two? as it is specify in 
>ffoplsaa.itp file 
>what about GROMOS96 force field, it is mention in manual (Chapter 4 page 
>no 75) it also scale down the LJ-14 repulsion term . 
>what I understood by manual that It uses separate parameter for LJ-14 
>interaction Is it is correct? If yes then It uses separate parameters only 
>for LJ repulsive term or all the non bonded terms i.e.  LJ repulsive,LJ 
>attractive and for coulomb term? 

The .itp file for your molecules will have the information that you are after.
1. The [ pairs ] section is a list that defines what 1-4 interactions exist. If 
a 1-4 pair is not in the [ pairs ] section, LJ-14 and Coulomb-14 interactions 
will not be included in the energies.

**That's a good test for you right there. Remove all entries from the [ pairs ] 
section and your 1-4 energies should drop to zero.

2. The charges for 1-4 interactions are the normal ones, and FudgeQQ will be 
applied.
3. The LJ sigma / epsilon parameters will be taken from [ pairs ] if they are 
there, or (second in hiearchy) from [ pairtypes ] if they are there, or (third 
in hiearchy) generated from the regular non-bonded parameters if gen-pairs=yes. 
In this third case, FudgeLJ is applied.

Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but these 
apply to the information outlined above. For example, gen-pairs does NOT mean 
"generate a [ pairs ] section for the molecule." Instead, it means "If LJ-14 
epsilon and sigma are not present in a [ pairs ] section entry, and that type 
of 
interaction is not explicitly formulated in [ pairtypes ], then it is 
permissible to use the regular non-bonded parameters, and in that case scale 
them by FudgeLJ."

OPLS-AA uses gen-pairs=yes, Force-fields that use gen-pairs=no (GROMOS96 I 
think) will have a very large [ pairtypes ] section. FudgeLJ is not used when 
gen-pairs=no, but FudgeQQ is always used. Note that it is perfectly reasonable 
to scale the 1-4 FudgeQQ/LJ and set gen-pairs=no.

If there is still misunderstanding, do a search for {pairs pairtypes}. 

Also, if your main concern is ensuring that you don't have any 1-4 interactions 
where you shouldn't then I would recommend drawing out your molecule and making 
sure that you don't have any RB dihedrals defined with an overlapping entry in 
the [ pairs ] section. However, this is not absolutely going to work because it 
gets complicated sometimes. Eg: I have yet to figure out exactly why things are 
treated as they are in the [ pairs ] section for two non-RB double-bonded 
carbons in the middle of a long chain of RB carbons :: more specifically I am 
referring to lipid acyl chains with a double bond (for example pope.itp from 
Dr. 
Tieleman).

Chris.
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