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

2014-01-15 Thread 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

2014-01-15 Thread 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 jalem...@vt.edu 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

 ==
 --
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 Support/Mailing_Lists/GMX-Users_List before posting!

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-- 
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

2014-01-15 Thread 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

==
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