[gmx-developers] [Fwd: coulomb SR in 3.3cvs]

[David]

-------- Forwarded Message --------
From: Michel Cuendet <michel.cuendet at epfl.ch>
Reply-To: michel.cuendet at epfl.ch
To: David <spoel at xray.bmc.uu.se>
Subject: [Fwd: Re: [gmx-developers] [Fwd: coulomb SR in 3.3cvs]]
Date: Wed, 27 Jul 2005 14:11:05 +0200
Hi David,

Are there any news about the interesting Coulomb SR feature of gromacs 
3.3.cvs ?

Has anybody else observed the phenomenon ? I have seen it on two 
different systems.

I'd really like to know if I can go on using that version on my itaniums 
or not   :-S

Thanks !

Michel

-------- Original Message --------
Subject: 	Re: [gmx-developers] [Fwd: coulomb SR in 3.3cvs]
Date: 	Tue, 19 Jul 2005 15:14:07 +0200
From: 	Michel Cuendet <michel.cuendet at epfl.ch>
To: 	David <spoel at xray.bmc.uu.se>
CC: 	Discussion list for GROMACS development <gmx-developers at gromacs.org>
References: 
<Pine.LNX.4.44.0507181650400.9527-100000 at rembrandt.bmc.uu.se> 
<42DBCB60.3040803 at epfl.ch> <1121707961.7165.4.camel at localhost.localdomain>


Hi David,

>You should only compare the first step. The virial (pressure) will tell
>you whether forces are correct.
>
Allright, here it is :

-------------------------------------------------------------------------
First step:  Virial XX, YY, ZZ, EKin, Pressure :
3.2.1 :
   0.000000  68261.312500  75314.625000  68934.000000   216638.687500   
44.703457
3.3 :
   0.000000  68055.515625  75127.718750  69873.421875   218547.906250   
75.353340

-------------------------------------------------------------------------
Energies at first step :
@ s0 legend "G96Bond"
@ s1 legend "G96Angle"
@ s2 legend "Proper Dih."
@ s3 legend "Improper Dih."
@ s4 legend "LJ-14"
@ s5 legend "Coulomb-14"
@ s6 legend "LJ (SR)"
@ s7 legend "Coulomb (SR)"
@ s8 legend "Coul. recip."
@ s9 legend "Potential"

3.2.1  :
 0.000000  6909.100586  10166.941406  4475.063477  3269.806641  
820.055969  62880.343750  166514.671875  -1203442.750000  
-188707.640625  -1137114.375000
3.3 :
 0.000000  6909.088867  10166.948242  4475.061523  3269.804443  
820.041321  62880.359375  166517.578125  -1203541.000000  
-188709.156250  -1137211.375000
-------------------------------------------------------------------------

We see that the energies are all accurate at least up to the 5th digit 
(can we expect more frome single precision?). The virials diverge 
already from the third digit. So do the kinetic energies, and the 
pressures differ...

I don't know what conclusions to draw from that.

Thanks for your assistance.

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                         	Phone : +41 1 693 0324
lcbcpc21.epfl.ch/~mitch                        +41  1 633 4194
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++




-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++