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

albitauro at virgilio.it albitauro at virgilio.it
Thu Oct 1 09:57:10 CEST 2009

```Ok! Thanks.
My table should be correct...yes in the third column I have the forces.
In any case, my simulations with the same potential (analytical or numerical) still give results which are largely different.
Do you have any further suggestions?
Thank you very very much!

AM

----Messaggio originale----

Da: gmx3 at hotmail.com

Data: 1-ott-2009 7.00 AM

A: <albitauro at virgilio.it>, "Discussion list for GROMACS users"<gmx-users at gromacs.org>

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

-->

Hi,

You can put the force constant in the table and use a force constant of 1 in the topology,
or only put the 1/2 in the table and put the force constant in the topolgy, the effect is the same.

The points in the table_b.xvg file should be equally spaced.
grompp assumes equal spacing, but does not check this.

Also note that you have to give the force, the negative of the derivative.
But I assume you have done this, as I have built a check in grompp to give
a warning when the potential and the force are inconsistent.

Berk

Date: Thu, 1 Oct 2009 08:53:51 +0200
From: albitauro at virgilio.it
To: gmx-users at gromacs.org
Subject: R: RE: R: Re: R:[gmx-users] Tabulated potential	- Problem

Hi Berk,
the tabulated potential I used (the file table_b.xvg) is exactly the function
V(R)=1/2 *k*(R-R0)^2 in numerical form. I printed in the first column the R variable from 0 to 2 nm in step of 0.001 nm,
on the second column the associated  V(R) value (KJ/mol) and in the third column its derivatives. With this choice I chose the force constant
k (that must be defined for tabulated function) to 1.0.
my numerical potential should be already correct in dimensions and units and so I guessed that k should have been equal to 1.0.
Further, I use the occasion to ask you also if the x points in the table "should be uniformly spaced" as reported in the manual so that there are no problems even if it's not so or they "must be uniformly spaced" to obtain the correct results.
Thank you,

AM

----Messaggio originale----

Da: gmx3 at hotmail.com

Data: 30-set-2009 1.36 PM

A: <albitauro at virgilio.it>, "Discussion list for GROMACS users"<gmx-users at gromacs.org>

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

Hi,

Are you really sure you entered the tabulated potential correctly?
There is for instance the pre-factor 1/2 in front of the harmonic potential,
which you will have to add explicitly, either in the table or in the force constant.

Berk

Date: Wed, 30 Sep 2009 14:33:31 +0200
From: albitauro at virgilio.it
To: gmx-users at gromacs.org
Subject: R: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential	-	Problem

Dear Mark,
unfortunately the differences I was speaking about are very consistent.
I am simulating a short chain with MARTINI CG force field:
with an analytical harmonic potential the chain becomes a random coil, when using the same potential but in tabulated numerical form the chain remains extended and only slightly distorted from linearity. All the parameters of the simulation (box sizes, mdp option...) are the same.
I will try  the options for mdrun.
Thank you,

Alberto

----Messaggio originale----
Da: Mark.Abraham at anu.edu.au
Data: 30-set-2009 12.15 PM
A: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
Ogg: Re: R: RE: R: RE: R: RE: R: RE: [gmx-users] Tabulated potential -	Problem

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
>
>
> 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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