R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem

[Mark Abraham]

albitauro at virgilio.it wrote:
> I changed bond type to 8.
> In any case the two MD simulations (same harmonic potential but in 
> analytical form vs tabulated form) gives different results.
> All the pararameters of the simulation are the same.

Slight differences will be normal unless you're running with "mdrun 
-reprod." Even then, there will be small differences between tabulated 
and non-tabulated. If you really want to be sure, you should consider 
doing an "mdrun -rerun -reprod" so that you are calculating the same 
quantities on the same inputs.

Mark

> ----Messaggio originale----
> Da: gmx3 at hotmail.com
> Data: 29-set-2009 3.54 PM
> A: <albitauro at virgilio.it>, "Discussion list for GROMACS 
> users"<gmx-users at gromacs.org>
> Ogg: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
> 
> No.
> 
> The ONLY difference between bonds type 8 and type 9 is that type 8 
> generates exclusions
> while type 9 does not (see table 5.4 in the manual).
> Simply changing from type 9 to 8 will generate the exclusions.
> 
> Berk
> 
> ------------------------------------------------------------------------
> Date: Tue, 29 Sep 2009 17:52:03 +0200
> From: albitauro at virgilio.it
> To: gmx-users at gromacs.org
> Subject: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
> 
> In my simulation I used bond type 9 because I was convinced that 1-2 LJ 
> interaction would have been excluded  in any case as default for bond 
> stretching interaction. After my simulations it seems not and so I 
> suppose that I must use bond type 8 and list the exclusion in the 
> itp...Right?
> 
> Alberto  
> 
> ----Messaggio originale----
> Da: gmx3 at hotmail.com
> Data: 29-set-2009 2.15 PM
> A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Ogg: RE: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
> 
> Are you really sure about this and that this is with bond type 8?
> 
> The whole point of having a tabulated bond type 8 and 9
> is that 8 does generate exclusions and 9 does not.
> 
> Berk
> 
> ------------------------------------------------------------------------
> Date: Tue, 29 Sep 2009 14:17:37 +0200
> From: albitauro at virgilio.it
> To: gmx-users at gromacs.org
> Subject: R: RE: R: RE: [gmx-users] Tabulated potential - Problem
> 
> Hi,
> 
> in order to check further which kind of problems are present when using
> tabulated potential, I carried out two simulations on the same system by 
> using the same harmonic
> potential for bond stretching but either in analytical form or in 
> tabulated form respectively. The
> results of the two simulations are different!
> I repeated the calculationis on just two bonded particles and I verified 
> that when using
> analytical stretching potentials 1-2 LJ interactions are excluded while they
> are not excluded when using tabulated potential.
> Am I right?
> 
> This should mean that I have to use a function type 8 and list 
> explicitly the elements of the [
> exclusions ] field or is there another method?
> 
> Thanks
> 
> Alberto
> 
> ----Messaggio originale----
> Da: gmx3 at hotmail.com
> Data: 25-set-2009 12.27 PM
> A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Ogg: RE: R: RE: [gmx-users] Tabulated potential - Problem
> 
> Your system could be unstable.
> You can check for large forces with mdrun -pforce
> I don't know what a reasonable range of forces is, you can try 5000.
> If you have instabilities, you should get large forces printed
> before you get the fatal error.
> 
> Berk
> 
> 
> ------------------------------------------------------------------------
> Date: Fri, 25 Sep 2009 14:10:08 +0200
> From: albitauro at virgilio.it
> To: gmx-users at gromacs.org
> Subject: R: RE: [gmx-users] Tabulated potential - Problem
> 
> Unfortunately, my box sizes are not close to 23. I also carried out 
> calculations switching off PBC or on much smaller systems.
> I received always the same error.
> I tried also a geometry optimization. It finished without warnings nor 
> errors: anyway the potential energy changed only very slightly during 
> the simulation with too large values.
> 
> Thanks
> 
> AM
> 
> ----Messaggio originale----
> Da: gmx3 at hotmail.com
> Data: 24-set-2009 11.29 AM
> A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Ogg: RE: [gmx-users] Tabulated potential - Problem
> 
> This is not nonsense, it is exactly what is says.
> The distance between two atoms is more than 10 times as large as your 
> table length.
> 
> Maybe you are somehow having issues with periodic boundary conditions.
> Is you box size close to 23?
> 
> Berk
> 
> 
> ------------------------------------------------------------------------
> Date: Thu, 24 Sep 2009 12:32:36 +0200
> From: albitauro at virgilio.it
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Tabulated potential - Problem
> 
> Hi,
> 
> I'm trying to carry out a CG simulation and I'm using
> a tabulated potential for a bond stretching term.
> My MD simulations stops immediately with the error message:
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: bondfree.c, line: 1772
> 
> Fatal error:
> A tabulated bond interaction table number 0 is out of the table range: r 
> 23.678833, between table indices 12069 and 12070, table length 1020
> -------------------------------------------------------
> 
> This should mean that some distances are beyond table length (as 
> reported in the manual) but this is
> nonsense considering my input files and topology.
> 
> Do you have any suggestion?
> Thanks!
> 
> AM
> 
> 
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