Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-09 Thread sulatha M. S 
Dear Rainer,

Thankyou very much. I read the abstract of this paper and it says torsional
parameters fro alkanes have been updated. I do not have access to full
contents of this paper, so could not get it.
Thanks again.

Sulatha

On Wed, Feb 9, 2011 at 2:27 PM, Rainer Boeckmann <
rainer.boeckm...@biologie.uni-erlangen.de> wrote:

> Dear Sulatha,
>
> these are probably the more recent parameters from
>
> Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and
> liquid-state properties of
> 8esters, nitriles, and nitro compounds with the opls-aa force field. J.
> Comput. Chem. 22:1340–
> 1352.
>
> Best
> Rainer
>
> On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:
>
> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121,
> 20, 4831, 1999), the aliphatic torsional parameters are the same as those
> from 1996. here are the values,
>
>
>V1
> V2V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
>
> HC-CT-CT-CT  0.0000.0000.366
>
> HC-CT-CT-HC 0.000 0.000   0.318
>
>
> Values calculated from the equation given in p.62 of the manual in kJ/mol
> are
>
>  c0   c1
>   c2 c3
> CT-CT-CT-CT 3.56686-1.88907
> 0.65688-2.33467
>
> HC-CT-CT-CT  0.66526   1.99577
> 0.000 -2.66102
>
> HC-CT-CT-HC 0.76567-2.29702   0.000
> -3.06269
>
> and the values given in ffoplsaabon.itp are:
>
> CT-CT-CT-CT 2.9288-1.46440.2092
>   -1.6736
>
> HC-CT-CT-CT 0.6276   1.88280
> 0.000  -2.5104
>
> HC-CT-CT-HC 0.62761.8828
> 0.000   -2.5104
>
> So there is a difference. Which of these is correct ? Any help is highly
> appreciated.
>
> Sulatha
>
>
>
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
>
>> There is no error. The alkane dihedral parameters were updated in 1999,
>> and differ from those originally published in 1996.
>>
>> Andrew
>>
>> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
>>
>>> Hi all,
>>>
>>> Hi
>>>
>>>
>>>
>>> I've converted the OPLS-AA torsional potential parameters for the
>>>
>>> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>>>
>>> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>>>
>>> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>>>
>>> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>>>
>>> that the calculated values are different.
>>>
>>>
>>>
>>> A previous post to the gmx-users mailing list on March 27, 2008,
>>>
>>> pointed out this issue for the H-C-C-H torsional potential but there was no 
>>> response to that.
>>>
>>>
>>>
>>> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>>>
>>> is there a newer set of OPLS-AA parameters?
>>>
>>>
>>>
>>> For the OPLS-AA parameters (in kcal/mol), I used:
>>>
>>>
>>>
>>> dihedral  V1  V2 V3
>>>
>>> C-C-C-C1.740  -0.157 0.279
>>>
>>> C-C-C-H 0.0  0.00.366
>>>
>>> H-C-C-H 0.0  0.00.318
>>>
>>>
>>>
>>> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
>>>
>>> C-C-C-H 0.66526   1.99577 0.0   -2.661024
>>>
>>> H-C-C-H 0.76567   -2.297020.0   -3.06269
>>>
>>>
>>>
>>> the parameters in the ffoplsaabon.itp file are:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
>>>
>>> C-C-C-H   0.6276   1.882800.0   -2.5104
>>>
>>> H-C-C-H   0.6276   1.8828  0.0   -2.5104
>>>
>>>
>>>
>>> Thankyou for any clarification.
>>>
>>> Sulatha
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send i

Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-09 Thread Rainer Boeckmann 
Dear Sulatha,

these are probably the more recent parameters from

Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and 
liquid-state properties of
8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. 
Chem. 22:1340–
1352.

Best
Rainer

On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:

> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 
> 4831, 1999), the aliphatic torsional parameters are the same as those from 
> 1996. here are the values,
>  
> 
>V1V2   
>  V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
> 
> HC-CT-CT-CT  0.0000.0000.366
> 
> HC-CT-CT-HC 0.000 0.000   0.318
> 
> 
> Values calculated from the equation given in p.62 of the manual in kJ/mol are 
> 
>  c0   c1  
>  c2 c3
> CT-CT-CT-CT 3.56686-1.889070.65688
> -2.33467
> 
> HC-CT-CT-CT  0.66526   1.995770.000   
>   -2.66102
> 
> HC-CT-CT-HC 0.76567-2.29702   0.000   
>   -3.06269
> 
> and the values given in ffoplsaabon.itp are:
> 
> CT-CT-CT-CT 2.9288-1.46440.2092   
> -1.6736
> 
> HC-CT-CT-CT 0.6276   1.88280   0.000  
> -2.5104
> 
> HC-CT-CT-HC 0.62761.8828   0.000  
>  -2.5104
> 
> So there is a difference. Which of these is correct ? Any help is highly 
> appreciated.
> 
> Sulatha
> 
> 
> 
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
> There is no error. The alkane dihedral parameters were updated in 1999, and 
> differ from those originally published in 1996.
> 
> Andrew
> 
> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
> Hi all,
> Hi
>  
> I've converted the OPLS-AA torsional potential parameters for the
> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) 
> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
> that the calculated values are different.
>  
> A previous post to the gmx-users mailing list on March 27, 2008,
> pointed out this issue for the H-C-C-H torsional potential but there was no 
> response to that.
>  
> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
> is there a newer set of OPLS-AA parameters?
>  
> For the OPLS-AA parameters (in kcal/mol), I used:
>  
> dihedral  V1  V2 V3
> C-C-C-C1.740  -0.157 0.279
> C-C-C-H 0.0  0.00.366
> H-C-C-H 0.0  0.00.318
>  
> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
> C-C-C-H 0.66526   1.99577 0.0   -2.661024
> H-C-C-H 0.76567   -2.297020.0   -3.06269
>  
> the parameters in the ffoplsaabon.itp file are:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
> C-C-C-H   0.6276   1.882800.0   -2.5104
> H-C-C-H   0.6276   1.8828  0.0   -2.5104
> 
> 
> Thankyou for any clarification.
> 
> Sulatha
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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> 
> 
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> 
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-09 Thread Rainer Boeckmann 
Dear Sulatha,

these are probably the more recent parameters from

Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and 
liquid-state properties of
8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. 
Chem. 22:1340–
1352.

Best
Rainer



On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:

> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 
> 4831, 1999), the aliphatic torsional parameters are the same as those from 
> 1996. here are the values,
>  
> 
>V1V2   
>  V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
> 
> HC-CT-CT-CT  0.0000.0000.366
> 
> HC-CT-CT-HC 0.000 0.000   0.318
> 
> 
> Values calculated from the equation given in p.62 of the manual in kJ/mol are 
> 
>  c0   c1  
>  c2 c3
> CT-CT-CT-CT 3.56686-1.889070.65688
> -2.33467
> 
> HC-CT-CT-CT  0.66526   1.995770.000   
>   -2.66102
> 
> HC-CT-CT-HC 0.76567-2.29702   0.000   
>   -3.06269
> 
> and the values given in ffoplsaabon.itp are:
> 
> CT-CT-CT-CT 2.9288-1.46440.2092   
> -1.6736
> 
> HC-CT-CT-CT 0.6276   1.88280   0.000  
> -2.5104
> 
> HC-CT-CT-HC 0.62761.8828   0.000  
>  -2.5104
> 
> So there is a difference. Which of these is correct ? Any help is highly 
> appreciated.
> 
> Sulatha
> 
> 
> 
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
> There is no error. The alkane dihedral parameters were updated in 1999, and 
> differ from those originally published in 1996.
> 
> Andrew
> 
> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
> Hi all,
> Hi
>  
> I've converted the OPLS-AA torsional potential parameters for the
> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) 
> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
> that the calculated values are different.
>  
> A previous post to the gmx-users mailing list on March 27, 2008,
> pointed out this issue for the H-C-C-H torsional potential but there was no 
> response to that.
>  
> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
> is there a newer set of OPLS-AA parameters?
>  
> For the OPLS-AA parameters (in kcal/mol), I used:
>  
> dihedral  V1  V2 V3
> C-C-C-C1.740  -0.157 0.279
> C-C-C-H 0.0  0.00.366
> H-C-C-H 0.0  0.00.318
>  
> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
> C-C-C-H 0.66526   1.99577 0.0   -2.661024
> H-C-C-H 0.76567   -2.297020.0   -3.06269
>  
> the parameters in the ffoplsaabon.itp file are:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
> C-C-C-H   0.6276   1.882800.0   -2.5104
> H-C-C-H   0.6276   1.8828  0.0   -2.5104
> 
> 
> Thankyou for any clarification.
> 
> Sulatha
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-08 Thread sulatha M. S 
Sorry for not giving the manual version earlier. P. 63 of manual 4.0 is what
I am referring to. The equations relate to converting the OPLS torsional
parameters to RB parameters in GROMACS with the OPLS ff.

The equations are
C0 = V0+V2+0.5(V1+V3)
C1= 0.5(3 * V3-V1)
C2= -V2 + 4 * V4
C3= -2 * V3
C4= -4 * V4

Thanks
Sulatha

On Wed, Feb 9, 2011 at 11:31 AM, Mark Abraham wrote:

>  On 9/02/2011 4:48 PM, sulatha M. S wrote:
>
> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121,
> 20, 4831, 1999), the aliphatic torsional parameters are the same as those
> from 1996. here are the values,
>
>
>V1
> V2V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
>
> HC-CT-CT-CT  0.0000.0000.366
>
> HC-CT-CT-HC 0.000 0.000   0.318
>
>
> Values calculated from the equation given in p.62 of the manual in kJ/mol
> are
>
>
> I can see nothing relevant on p62 of the 4.5 manual. When giving references
> to literature that exists in multiple versions, please be very precise.
> Giving details such as the manual version number, page number, equation
> number and description of the relationship described in the equation will
> make it much more likely that someone will (want to) (be able to) help you.
>
> Mark
>
>
>
>  c0   c1
>   c2 c3
> CT-CT-CT-CT 3.56686-1.88907
> 0.65688-2.33467
>
> HC-CT-CT-CT  0.66526   1.99577
> 0.000 -2.66102
>
> HC-CT-CT-HC 0.76567-2.29702   0.000
> -3.06269
>
> and the values given in ffoplsaabon.itp are:
>
> CT-CT-CT-CT 2.9288-1.46440.2092
>   -1.6736
>
> HC-CT-CT-CT 0.6276   1.88280
> 0.000  -2.5104
>
> HC-CT-CT-HC 0.62761.8828
> 0.000   -2.5104
>
> So there is a difference. Which of these is correct ? Any help is highly
> appreciated.
>
> Sulatha
>
>
>
>  On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
>
>> There is no error. The alkane dihedral parameters were updated in 1999,
>> and differ from those originally published in 1996.
>>
>> Andrew
>>
>>  On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S wrote:
>>
>>>  Hi all,
>>>
>>> Hi
>>>
>>>
>>>
>>> I've converted the OPLS-AA torsional potential parameters for the
>>>
>>> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>>>
>>> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>>>
>>> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>>>
>>> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>>>
>>> that the calculated values are different.
>>>
>>>
>>>
>>> A previous post to the gmx-users mailing list on March 27, 2008,
>>>
>>> pointed out this issue for the H-C-C-H torsional potential but there was no 
>>> response to that.
>>>
>>>
>>>
>>> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>>>
>>> is there a newer set of OPLS-AA parameters?
>>>
>>>
>>>
>>> For the OPLS-AA parameters (in kcal/mol), I used:
>>>
>>>
>>>
>>> dihedral  V1  V2 V3
>>>
>>> C-C-C-C1.740  -0.157 0.279
>>>
>>> C-C-C-H 0.0  0.00.366
>>>
>>> H-C-C-H 0.0  0.00.318
>>>
>>>
>>>
>>> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
>>>
>>> C-C-C-H 0.66526   1.99577 0.0   -2.661024
>>>
>>> H-C-C-H 0.76567   -2.297020.0   -3.06269
>>>
>>>
>>>
>>> the parameters in the ffoplsaabon.itp file are:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
>>>
>>> C-C-C-H   0.6276   1.882800.0   -2.5104
>>>
>>> H-C-C-H   0.6276   1.8828  0.0   -2.5104
>>>
>>>
>>>
>>> Thankyou for any clarification.
>>>
>>> Sulatha
>>>
>>>  --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.o

Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-08 Thread Mark Abraham 

On 9/02/2011 4:48 PM, sulatha M. S wrote:
I looked at the the paper published in 1999, ( Jorgensen et al JACS, 
121, 20, 4831, 1999), the aliphatic torsional parameters are the same 
as those from 1996. here are the values,



   V1
V2V3 (kcal/mol)

CT-CT-CT-CT  1.740   -0.157 0.279

HC-CT-CT-CT  0.0000.0000.366

HC-CT-CT-HC 0.000 0.000   0.318


Values calculated from the equation given in p.62 of the manual in 
kJ/mol are


I can see nothing relevant on p62 of the 4.5 manual. When giving 
references to literature that exists in multiple versions, please be 
very precise. Giving details such as the manual version number, page 
number, equation number and description of the relationship described in 
the equation will make it much more likely that someone will (want to) 
(be able to) help you.


Mark



 c0   c1 
  c2 c3
CT-CT-CT-CT 3.56686-1.88907
0.65688-2.33467


HC-CT-CT-CT  0.66526   1.99577
0.000 -2.66102


HC-CT-CT-HC 0.76567-2.29702   
0.000 -3.06269


and the values given in ffoplsaabon.itp are:

CT-CT-CT-CT 2.9288-1.4644
0.2092   -1.6736


HC-CT-CT-CT 0.6276   1.88280   
0.000  -2.5104


HC-CT-CT-HC 0.62761.8828   
0.000   -2.5104


So there is a difference. Which of these is correct ? Any help is 
highly appreciated.


Sulatha



On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch > wrote:


There is no error. The alkane dihedral parameters were updated in
1999, and differ from those originally published in 1996.

Andrew

On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mailto:mssula...@gmail.com>> wrote:

Hi all,

Hi

  


I've converted the OPLS-AA torsional potential parameters for the

alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),

C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the

OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)

to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found

that the calculated values are different.

  


A previous post to the gmx-users mailing list on March 27, 2008,

pointed out this issue for the H-C-C-H torsional potential but there 
was no response to that.

  


Does anyone know if there is an error in the ffoplsaabon.itp file? Or

is there a newer set of OPLS-AA parameters?

  


For the OPLS-AA parameters (in kcal/mol), I used:

  


dihedral   V1   V2  V3

C-C-C-C 1.740   -0.157  0.279

C-C-C-H  0.0   0.0 0.366

H-C-C-H  0.0   0.0 0.318

  


from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) 
as:

  


dihedral   C0C1  C2C3

C-C-C-C 3.56686-1.8890760.65688   -2.33467

C-C-C-H  0.665261.99577  0.0-2.661024

H-C-C-H  0.76567-2.29702 0.0-3.06269

  


the parameters in the ffoplsaabon.itp file are:

  


dihedral   C0   C1  C2C3

C-C-C-C2.9288   -1.4644   0.2092  -1.6736

C-C-C-H0.62761.88280 0.0-2.5104

H-C-C-H0.62761.8828   0.0-2.5104



Thankyou for any clarification.

Sulatha

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Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-08 Thread sulatha M. S 
I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121,
20, 4831, 1999), the aliphatic torsional parameters are the same as those
from 1996. here are the values,


   V1
V2V3 (kcal/mol)
CT-CT-CT-CT  1.740   -0.157 0.279

HC-CT-CT-CT  0.0000.0000.366

HC-CT-CT-HC 0.000 0.000   0.318


Values calculated from the equation given in p.62 of the manual in kJ/mol
are

 c0   c1
  c2 c3
CT-CT-CT-CT 3.56686-1.88907
0.65688-2.33467

HC-CT-CT-CT  0.66526   1.99577
0.000 -2.66102

HC-CT-CT-HC 0.76567-2.29702   0.000
-3.06269

and the values given in ffoplsaabon.itp are:

CT-CT-CT-CT 2.9288-1.46440.2092
  -1.6736

HC-CT-CT-CT 0.6276   1.88280
0.000  -2.5104

HC-CT-CT-HC 0.62761.8828   0.000
  -2.5104

So there is a difference. Which of these is correct ? Any help is highly
appreciated.

Sulatha



On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:

> There is no error. The alkane dihedral parameters were updated in 1999, and
> differ from those originally published in 1996.
>
> Andrew
>
> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
>
>> Hi all,
>>
>> Hi
>>
>>
>>
>> I've converted the OPLS-AA torsional potential parameters for the
>>
>> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>>
>> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>>
>> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>>
>> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>>
>> that the calculated values are different.
>>
>>
>>
>> A previous post to the gmx-users mailing list on March 27, 2008,
>>
>> pointed out this issue for the H-C-C-H torsional potential but there was no 
>> response to that.
>>
>>
>>
>> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>>
>> is there a newer set of OPLS-AA parameters?
>>
>>
>>
>> For the OPLS-AA parameters (in kcal/mol), I used:
>>
>>
>>
>> dihedral  V1  V2 V3
>>
>> C-C-C-C1.740  -0.157 0.279
>>
>> C-C-C-H 0.0  0.00.366
>>
>> H-C-C-H 0.0  0.00.318
>>
>>
>>
>> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>>
>>
>>
>> dihedral  C0  C1 C2   C3
>>
>> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
>>
>> C-C-C-H 0.66526   1.99577 0.0   -2.661024
>>
>> H-C-C-H 0.76567   -2.297020.0   -3.06269
>>
>>
>>
>> the parameters in the ffoplsaabon.itp file are:
>>
>>
>>
>> dihedral  C0  C1 C2   C3
>>
>> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
>>
>> C-C-C-H   0.6276   1.882800.0   -2.5104
>>
>> H-C-C-H   0.6276   1.8828  0.0   -2.5104
>>
>>
>>
>> Thankyou for any clarification.
>>
>> Sulatha
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] OPLS and RB parameters in GROMACS

2011-02-08 Thread Andrew Paluch 
There is no error. The alkane dihedral parameters were updated in 1999, and
differ from those originally published in 1996.

Andrew

On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:

> Hi all,
>
> Hi
>
>
>
> I've converted the OPLS-AA torsional potential parameters for the
>
> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>
> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>
> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>
> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>
> that the calculated values are different.
>
>
>
> A previous post to the gmx-users mailing list on March 27, 2008,
>
> pointed out this issue for the H-C-C-H torsional potential but there was no 
> response to that.
>
>
>
> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>
> is there a newer set of OPLS-AA parameters?
>
>
>
> For the OPLS-AA parameters (in kcal/mol), I used:
>
>
>
> dihedral  V1  V2 V3
>
> C-C-C-C1.740  -0.157 0.279
>
> C-C-C-H 0.0  0.00.366
>
> H-C-C-H 0.0  0.00.318
>
>
>
> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>
>
>
> dihedral  C0  C1 C2   C3
>
> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
>
> C-C-C-H 0.66526   1.99577 0.0   -2.661024
>
> H-C-C-H 0.76567   -2.297020.0   -3.06269
>
>
>
> the parameters in the ffoplsaabon.itp file are:
>
>
>
> dihedral  C0  C1 C2   C3
>
> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
>
> C-C-C-H   0.6276   1.882800.0   -2.5104
>
> H-C-C-H   0.6276   1.8828  0.0   -2.5104
>
>
>
> Thankyou for any clarification.
>
> Sulatha
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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>
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[gmx-users] OPLS and RB parameters in GROMACS

2011-02-08 Thread sulatha M. S 
Hi all,

Hi



I've converted the OPLS-AA torsional potential parameters for the

alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),

C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the

OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)

to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found

that the calculated values are different.



A previous post to the gmx-users mailing list on March 27, 2008,

pointed out this issue for the H-C-C-H torsional potential but there
was no response to that.



Does anyone know if there is an error in the ffoplsaabon.itp file? Or

is there a newer set of OPLS-AA parameters?



For the OPLS-AA parameters (in kcal/mol), I used:



dihedral  V1  V2 V3

C-C-C-C1.740  -0.157 0.279

C-C-C-H 0.0  0.00.366

H-C-C-H 0.0  0.00.318



from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:



dihedral  C0  C1 C2   C3

C-C-C-C3.56686   -1.889076   0.65688   -2.33467

C-C-C-H 0.66526   1.99577 0.0   -2.661024

H-C-C-H 0.76567   -2.297020.0   -3.06269



the parameters in the ffoplsaabon.itp file are:



dihedral  C0  C1 C2   C3

C-C-C-C   2.9288  -1.4644  0.2092 -1.6736

C-C-C-H   0.6276   1.882800.0   -2.5104

H-C-C-H   0.6276   1.8828  0.0   -2.5104



Thankyou for any clarification.

Sulatha
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