[gmx-users] Calculation of Cv

[Saumyak Mukherjee]

Dear all,

I have written a FORTRAN 90 code to calculate Cv. Now I want to calculate
the Cv of protein. I ran the simulation with energygrps = Protein SOL. So I
have separate self and cross terms for all.

Which energy terms shall I include in calculation of Cv? Shall I take only
the "SR" terms or anything else?

Thanks and regards,
Saumyak

-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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Re: [gmx-users] Calculation of Cv

[Sunil Ghimire]

No sir.i want to know whether it is possible to obtain from energies and
enthalpy obtained from g_energy?
On 31 Aug 2015 19:57, "David van der Spoel"  wrote:

> On 31/08/15 14:15, Sunil Ghimire wrote:
>
>> Dear sir,
>>  Thanks for suggestion.This is the theoritical approach.I want to
>> known
>> how can we obtain Cv from the production run done with NVT ensemble? Is it
>> possible to obtain from g_energy ?
>>
> Have you tried?
>
> On 31 Aug 2015 17:18, "Justin Lemkul"  wrote:
>>
>>
>>>
>>> On 8/30/15 10:41 PM, Sunil Ghimire wrote:
>>>
>>> Dear sir,
How can we calculate the value  of Cv for noble gases?


 http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
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>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Calculation of Cv

[Marcelo Depólo]

2015-08-31 12:43 GMT-03:00 Sunil Ghimire :

> No sir.i want to know whether it is possible to obtain from energies and
> enthalpy obtained from g_energy?
>

The answer was just one google away:
http://manual.gromacs.org/programs/gmx-energy.html

Still, read about Heat Capacities calculations using g_energy and DoS
simulations.

On 31 Aug 2015 19:57, "David van der Spoel"  wrote:
>
> > On 31/08/15 14:15, Sunil Ghimire wrote:
> >
> >> Dear sir,
> >>  Thanks for suggestion.This is the theoritical approach.I want to
> >> known
> >> how can we obtain Cv from the production run done with NVT ensemble? Is
> it
> >> possible to obtain from g_energy ?
> >>
> > Have you tried?
> >
> > On 31 Aug 2015 17:18, "Justin Lemkul"  wrote:
> >>
> >>
> >>>
> >>> On 8/30/15 10:41 PM, Sunil Ghimire wrote:
> >>>
> >>> Dear sir,
> How can we calculate the value  of Cv for noble gases?
> 
> 
>  http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 629
> >>> University of Maryland, Baltimore
> >>> 20 Penn St.
> >>> Baltimore, MD 21201
> >>>
> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>> posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> > --
> > Gromacs Users mailing list
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> >
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>



-- 
Marcelo Depólo Polêto
Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)
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Re: [gmx-users] Calculation of Cv

[Justin Lemkul]

On 8/30/15 10:41 PM, Sunil Ghimire wrote:

Dear sir,
  How can we calculate the value  of Cv for noble gases?



http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Calculation of Cv

[David van der Spoel]

On 31/08/15 14:15, Sunil Ghimire wrote:

Dear sir,
 Thanks for suggestion.This is the theoritical approach.I want to known
how can we obtain Cv from the production run done with NVT ensemble? Is it
possible to obtain from g_energy ?

Have you tried?


On 31 Aug 2015 17:18, "Justin Lemkul"  wrote:




On 8/30/15 10:41 PM, Sunil Ghimire wrote:


Dear sir,
   How can we calculate the value  of Cv for noble gases?



http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/shegas.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Calculation of Cv

[Sunil Ghimire]

Dear sir,
 How can we calculate the value  of Cv for noble gases?
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