[gmx-users] LR electrostatics in single point energy calculations

[rajat desikan]

Hi All,
I was wondering about the long range electrostatics while calculating
single point energies. I did a cursory calculation for a protein in water
(PME) and found that the LR electrostatic terms were zero. I know that the
per-particle decomposition of the LR electrostatics is non trivial. I was
wondering if there is a way to do it in Gromacs?

Thanks,

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] LR electrostatics in single point energy calculations

[Justin Lemkul]

On 1/15/14, 7:14 AM, rajat desikan wrote:

Hi All,
I was wondering about the long range electrostatics while calculating
single point energies. I did a cursory calculation for a protein in water
(PME) and found that the LR electrostatic terms were zero. I know that the
per-particle decomposition of the LR electrostatics is non trivial. I was
wondering if there is a way to do it in Gromacs?



Was the Coul-recip term actually zero, or were you looking at Coul-LR?  The two 
terms mean very different things.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] LR electrostatics in single point energy calculations

[rajat desikan]

Hi Justin,

I used the following commands:

mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
gmxdump_mpi -e ener.edr > ener_readme

And in the dump of the ener_readme file, I have the following terms:

Coul-SR:Protein-Protein  -6.62324e+05
LJ-SR:Protein-Protein  -5.64854e+04
Coul-14:Protein-Protein   4.04345e+05
LJ-14:Protein-Protein   3.29438e+04

Coul-SR:Protein-POPC  -1.97403e+03
LJ-SR:Protein-POPC  -4.64531e+03
Coul-14:Protein-POPC   0.0e+00
LJ-14:Protein-POPC   0.0e+00

...etc

There is neither a Coul-recip nor a Coul-LR term. So, I was wondering about
it. The Coul-recip is the reciprocal space term in a Ewald summation
calculation, right? I want the total potential energy of the protein. How
would I go about that?

Thanks.



On Wed, Jan 15, 2014 at 7:39 PM, Justin Lemkul  wrote:

>
>
> On 1/15/14, 7:14 AM, rajat desikan wrote:
>
>> Hi All,
>> I was wondering about the long range electrostatics while calculating
>> single point energies. I did a cursory calculation for a protein in water
>> (PME) and found that the LR electrostatic terms were zero. I know that the
>> per-particle decomposition of the LR electrostatics is non trivial. I was
>> wondering if there is a way to do it in Gromacs?
>>
>>
> Was the Coul-recip term actually zero, or were you looking at Coul-LR?
>  The two terms mean very different things.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> 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.
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
Gromacs Users mailing list

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Re: [gmx-users] LR electrostatics in single point energy calculations

[Justin Lemkul]

On 1/15/14, 11:57 AM, rajat desikan wrote:

Hi Justin,
I meant the pairwise interaction energies and not the total potential energy (I
plan to define a 'interaction energy' by summing up all the individual terms). I
followed your argument on the total potential energy of the protein being a
function of the forcefield.

I need the interaction parameters along with the LR terms. I am wondering how to
do that.

g_energy also gives me only the SR and 14 options. Here is part of a snapshot of
the available options:

...
47  Box-Vel-ZZ  48  Coul-SR:Protein-Protein
49  LJ-SR:Protein-Protein   50  Coul-14:Protein-Protein
51  LJ-14:Protein-Protein52  Coul-SR:Protein-POPC
53  LJ-SR:Protein-POPC54  Coul-14:Protein-POPC
55  LJ-14:Protein-POPC 56  Coul-SR:Protein-SOL
...etc



There are no "LR" terms unless you use a twin-range cutoff scheme 
(http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy).  The PME mesh 
term is written to the Coul-recip term.  Decomposing it is not trivial.


-Justin



On Wed, Jan 15, 2014 at 10:17 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote:



On 1/15/14, 11:38 AM, rajat desikan wrote:

Hi Justin,

I used the following commands:

mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
gmxdump_mpi -e ener.edr > ener_readme

And in the dump of the ener_readme file, I have the following terms:

Coul-SR:Protein-Protein  -6.62324e+05
LJ-SR:Protein-Protein  -5.64854e+04
Coul-14:Protein-Protein   4.04345e+05
LJ-14:Protein-Protein   3.29438e+04

Coul-SR:Protein-POPC  -1.97403e+03
LJ-SR:Protein-POPC  -4.64531e+03
Coul-14:Protein-POPC   0.0e+00
LJ-14:Protein-POPC   0.0e+00

...etc

There is neither a Coul-recip nor a Coul-LR term. So, I was wondering
about it.
The Coul-recip is the reciprocal space term in a Ewald summation
calculation,
right? I want the total potential energy of the protein. How would I go
about that?


I won't go into why "the total potential energy of the protein" is complete
junk, because I explained all that last week.

I don't know what to expect from gmxdump, but you should probably be using
g_energy instead.


-Justin

--
==__

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.__edu
 | (410) 706-7441

==__




--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore


--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] LR electrostatics in single point energy calculations

[rajat desikan]

Hi Justin,
Thanks for the reply. So, must I use a separate .mdp file with infinite
cutoffs for both vdw and coulomb to get all the LR interactions correctly?
Can you give me specific pointers about the settings?



On Wed, Jan 15, 2014 at 11:20 PM, Justin Lemkul  wrote:

>
>
> On 1/15/14, 11:57 AM, rajat desikan wrote:
>
>> Hi Justin,
>>
>> I meant the pairwise interaction energies and not the total potential
>> energy (I
>> plan to define a 'interaction energy' by summing up all the individual
>> terms). I
>> followed your argument on the total potential energy of the protein being
>> a
>> function of the forcefield.
>>
>> I need the interaction parameters along with the LR terms. I am wondering
>> how to
>> do that.
>>
>> g_energy also gives me only the SR and 14 options. Here is part of a
>> snapshot of
>> the available options:
>>
>> ...
>> 47  Box-Vel-ZZ  48  Coul-SR:Protein-Protein
>> 49  LJ-SR:Protein-Protein   50  Coul-14:Protein-Protein
>> 51  LJ-14:Protein-Protein52  Coul-SR:Protein-POPC
>> 53  LJ-SR:Protein-POPC54  Coul-14:Protein-POPC
>> 55  LJ-14:Protein-POPC 56  Coul-SR:Protein-SOL
>> ...etc
>>
>>
> There are no "LR" terms unless you use a twin-range cutoff scheme (
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy).  The
> PME mesh term is written to the Coul-recip term.  Decomposing it is not
> trivial.
>
> -Justin
>
>
>> On Wed, Jan 15, 2014 at 10:17 PM, Justin Lemkul > > wrote:
>>
>>
>>
>> On 1/15/14, 11:38 AM, rajat desikan wrote:
>>
>> Hi Justin,
>>
>> I used the following commands:
>>
>> mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
>> gmxdump_mpi -e ener.edr > ener_readme
>>
>> And in the dump of the ener_readme file, I have the following
>> terms:
>>
>> Coul-SR:Protein-Protein  -6.62324e+05
>> LJ-SR:Protein-Protein  -5.64854e+04
>> Coul-14:Protein-Protein   4.04345e+05
>> LJ-14:Protein-Protein   3.29438e+04
>>
>> Coul-SR:Protein-POPC  -1.97403e+03
>> LJ-SR:Protein-POPC  -4.64531e+03
>> Coul-14:Protein-POPC   0.0e+00
>> LJ-14:Protein-POPC   0.0e+00
>>
>> ...etc
>>
>> There is neither a Coul-recip nor a Coul-LR term. So, I was
>> wondering
>> about it.
>> The Coul-recip is the reciprocal space term in a Ewald summation
>> calculation,
>> right? I want the total potential energy of the protein. How
>> would I go
>> about that?
>>
>>
>> I won't go into why "the total potential energy of the protein" is
>> complete
>> junk, because I explained all that last week.
>>
>> I don't know what to expect from gmxdump, but you should probably be
>> using
>> g_energy instead.
>>
>>
>> -Justin
>>
>> --
>> ==__
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.__edu
>>  | (410) 706-7441
>>
>> ==__
>>
>>
>>
>>
>>
>> --
>> Rajat Desikan (Ph.D Scholar)
>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>> Dept. of Chemical Engineering,
>> Indian Institute of Science, Bangalore
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> 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.
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] LR electrostatics in single point energy calculations

[Justin Lemkul]

On 1/15/14, 4:18 PM, rajat desikan wrote:

Hi Justin,
Thanks for the reply. So, must I use a separate .mdp file with infinite cutoffs
for both vdw and coulomb to get all the LR interactions correctly? Can you give
me specific pointers about the settings?



Infinite cutoffs, zero steps, don't use constraints (so the coordinates don't 
change), then follow 
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
Gromacs Users mailing list

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