subject:"\[gmx\-users\] unit conversions"

Re: [gmx-users] unit conversions

2010-09-17 Thread Ramachandran G

Thank you for your clarification.
Rama

On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul  wrote:

>
>
> Ramachandran G wrote:
>
>> Thank you Justin,
>> You are right i am not comparing the same force field.
>>   But i am still curious to know the conversion factor for epsilon from
>> MOIL to gromacs(charmm)force field.
>> i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.
>>
>>
> If you are not comparing the same force fields, you are not likely to get
> the same answer.  I thought I identified the fact that the value you are
> referring to corresponds to the MOIL implementation of OPLS-UA, which has no
> relationship whatsoever to the Gromacs implementation of CHARMM.
>
> Dividing by 4.184 is the correct conversion factor for kcal->kJ.
>
> -Justin
>
> with regards,
>> Rama
>>
>>
>> On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Ramachandran G wrote:
>>
>>I understood from the gromacs manual the units for epsilon and
>>sigma are KJ/mol and nm  and the corresponding units in MOIL
>>Kcal/mol and Angstom. But when i checked for some atoms, the
>>epsilon values are not matching. i.e., for example i took the
>>value of epsilon value of S from gromacs 1.8828 and divided by
>>the conversion faction 4.184. The result is 0.45 but in MOIL the
>>value is 0.25. I also checked some other atoms like K,Na,Cl...
>>there also the values does not match.
>>
>>
>>Are you comparing the same force fields?  According to the MOIL
>>documentation, CHARMM is not implemented unless the user provides
>>it.  However, the epsilon value of OPLS-UA sulfur (1.046), when
>>converted to MOIL units (kcal/mol), is 0.25, which I assume is where
>>you're finding that value.
>>
>>-Justin
>>
>>If anybody knows where i am making mistake please teach me.
>>Thank you.
>>
>>with regards,
>>Rama
>>
>>On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Ramachandran G wrote:
>>
>>   Hi gmx-users,
>>  I would like to know the units conversion of epsilon,
>>sigma
>>   (from non-bonded, Van der Waal interaction)  from Charmm
>>or MOIL
>>   to gromacs.
>>   Thank you.
>>
>>
>>   My guess would be that each of the respective manuals would
>>discuss
>>   whatever unit conventions are utilized.  As far as Gromacs is
>>   concerned, Chapter 4 contains information about such matters, as
>>   well as Table 5.2 (and sections nearby).
>>
>>   -Justin
>>
>>   with regards,
>>   Rama
>>
>>
>>
>>   -- 
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   -- gmx-users mailing 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
>>
>>
>>
>>
>>-- Postdoctoral Research Scholar,
>>Department of Chemistry,
>>University of Nevada, Reno.
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing 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
>>

Re: [gmx-users] unit conversions

2010-09-17 Thread Justin A. Lemkul

Ramachandran G wrote:

Thank you Justin,
 You are right i am not comparing the same force field.
   But i am still curious to know the conversion factor for epsilon from 
MOIL to gromacs(charmm)force field.

i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.

If you are not comparing the same force fields, you are not likely to get the 
same answer.  I thought I identified the fact that the value you are referring 
to corresponds to the MOIL implementation of OPLS-UA, which has no relationship 
whatsoever to the Gromacs implementation of CHARMM.

Dividing by 4.184 is the correct conversion factor for kcal->kJ.

-Justin

with regards,
Rama

On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul > wrote:

Ramachandran G wrote:

I understood from the gromacs manual the units for epsilon and
sigma are KJ/mol and nm  and the corresponding units in MOIL
Kcal/mol and Angstom. But when i checked for some atoms, the
epsilon values are not matching. i.e., for example i took the
value of epsilon value of S from gromacs 1.8828 and divided by
the conversion faction 4.184. The result is 0.45 but in MOIL the
value is 0.25. I also checked some other atoms like K,Na,Cl...
there also the values does not match.

Are you comparing the same force fields?  According to the MOIL
documentation, CHARMM is not implemented unless the user provides
it.  However, the epsilon value of OPLS-UA sulfur (1.046), when
converted to MOIL units (kcal/mol), is 0.25, which I assume is where
you're finding that value.

-Justin

If anybody knows where i am making mistake please teach me.
Thank you.

with regards,
Rama

On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   Ramachandran G wrote:

   Hi gmx-users,
  I would like to know the units conversion of epsilon,
sigma
   (from non-bonded, Van der Waal interaction)  from Charmm
or MOIL
   to gromacs.
   Thank you.

   My guess would be that each of the respective manuals would
discuss
   whatever unit conventions are utilized.  As far as Gromacs is
   concerned, Chapter 4 contains information about such matters, as
   well as Table 5.2 (and sections nearby).

   -Justin

   with regards,
   Rama

   -- 

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   -- gmx-users mailing 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

-- 
Postdoctoral Research Scholar,

Department of Chemistry,
University of Nevada, Reno.

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

-- 
gmx-users mailing 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

--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT

Re: [gmx-users] unit conversions

2010-09-17 Thread Ramachandran G

Thank you Justin,
 You are right i am not comparing the same force field.
   But i am still curious to know the conversion factor for epsilon from
MOIL to gromacs(charmm)force field.
i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.

with regards,
Rama

On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul  wrote:

>
>
> Ramachandran G wrote:
>
>> I understood from the gromacs manual the units for epsilon and sigma are
>> KJ/mol and nm  and the corresponding units in MOIL Kcal/mol and Angstom. But
>> when i checked for some atoms, the epsilon values are not matching. i.e.,
>> for example i took the value of epsilon value of S from gromacs 1.8828 and
>> divided by the conversion faction 4.184. The result is 0.45 but in MOIL the
>> value is 0.25. I also checked some other atoms like K,Na,Cl... there also
>> the values does not match.
>>
>>
> Are you comparing the same force fields?  According to the MOIL
> documentation, CHARMM is not implemented unless the user provides it.
>  However, the epsilon value of OPLS-UA sulfur (1.046), when converted to
> MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that
> value.
>
> -Justin
>
>  If anybody knows where i am making mistake please teach me. Thank you.
>>
>> with regards,
>> Rama
>>
>> On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Ramachandran G wrote:
>>
>>Hi gmx-users,
>>   I would like to know the units conversion of epsilon, sigma
>>(from non-bonded, Van der Waal interaction)  from Charmm or MOIL
>>to gromacs.
>>Thank you.
>>
>>
>>My guess would be that each of the respective manuals would discuss
>>whatever unit conventions are utilized.  As far as Gromacs is
>>concerned, Chapter 4 contains information about such matters, as
>>well as Table 5.2 (and sections nearby).
>>
>>-Justin
>>
>>with regards,
>>Rama
>>
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing 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
>>
>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> University of Nevada, Reno.
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing 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
>



-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
-- 
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!
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Re: [gmx-users] unit conversions

2010-09-17 Thread Justin A. Lemkul




Ramachandran G wrote:
I understood from the gromacs manual the units for epsilon and sigma are 
KJ/mol and nm  and the corresponding units in MOIL Kcal/mol and Angstom. 
But when i checked for some atoms, the epsilon values are not matching. 
i.e., for example i took the value of epsilon value of S from gromacs 
1.8828 and divided by the conversion faction 4.184. The result is 0.45 
but in MOIL the value is 0.25. I also checked some other atoms like 
K,Na,Cl... there also the values does not match.




Are you comparing the same force fields?  According to the MOIL documentation, 
CHARMM is not implemented unless the user provides it.  However, the epsilon 
value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 
0.25, which I assume is where you're finding that value.


-Justin


If anybody knows where i am making mistake please teach me. Thank you.

with regards,
Rama

On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul > wrote:




Ramachandran G wrote:

Hi gmx-users,
   I would like to know the units conversion of epsilon, sigma
(from non-bonded, Van der Waal interaction)  from Charmm or MOIL
to gromacs.
Thank you.


My guess would be that each of the respective manuals would discuss
whatever unit conventions are utilized.  As far as Gromacs is
concerned, Chapter 4 contains information about such matters, as
well as Table 5.2 (and sections nearby).

-Justin

with regards,
Rama



-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
gmx-users mailing 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




--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing 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

Re: [gmx-users] unit conversions

2010-09-17 Thread Ramachandran G

I understood from the gromacs manual the units for epsilon and sigma are
KJ/mol and nm  and the corresponding units in MOIL Kcal/mol and Angstom. But
when i checked for some atoms, the epsilon values are not matching. i.e.,
for example i took the value of epsilon value of S from gromacs 1.8828 and
divided by the conversion faction 4.184. The result is 0.45 but in MOIL the
value is 0.25. I also checked some other atoms like K,Na,Cl... there also
the values does not match.

If anybody knows where i am making mistake please teach me. Thank you.

with regards,
Rama

On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul  wrote:

>
>
> Ramachandran G wrote:
>
>> Hi gmx-users,
>>I would like to know the units conversion of epsilon, sigma (from
>> non-bonded, Van der Waal interaction)  from Charmm or MOIL to gromacs.
>> Thank you.
>>
>>
> My guess would be that each of the respective manuals would discuss
> whatever unit conventions are utilized.  As far as Gromacs is concerned,
> Chapter 4 contains information about such matters, as well as Table 5.2 (and
> sections nearby).
>
> -Justin
>
>  with regards,
>> Rama
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing 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
>



-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
-- 
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!
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Re: [gmx-users] unit conversions

2010-09-17 Thread Justin A. Lemkul




Ramachandran G wrote:

Hi gmx-users,
I would like to know the units conversion of epsilon, sigma (from 
non-bonded, Van der Waal interaction)  from Charmm or MOIL to gromacs.

Thank you.



My guess would be that each of the respective manuals would discuss whatever 
unit conventions are utilized.  As far as Gromacs is concerned, Chapter 4 
contains information about such matters, as well as Table 5.2 (and sections nearby).


-Justin


with regards,
Rama




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing 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!
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[gmx-users] unit conversions

2010-09-17 Thread Ramachandran G

Hi gmx-users,
I would like to know the units conversion of epsilon, sigma (from
non-bonded, Van der Waal interaction)  from Charmm or MOIL to gromacs.
Thank you.

with regards,
Rama
-- 
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

Re: [gmx-users] unit conversions

Re: [gmx-users] unit conversions

Re: [gmx-users] unit conversions

Re: [gmx-users] unit conversions

Re: [gmx-users] unit conversions

Re: [gmx-users] unit conversions

[gmx-users] unit conversions

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