[gmx-users] a bit strange errors(Solved:Thanks to all)

[wuxiao]

Dear GMXers,

I have solved the questions posted previously. It is not the unit and the transformation but the use of f'(x) instead of -f'(x) that leads to the issues. Anyway, thanks a lot for your attention and some suggestions from Berk and Mark

Best wishes,

Chaofu Wu, Dr.
 


From: xiaowu759 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009 15:51:18 +0800



Dear Berk,
In fact, I calculated the potential and force from the analytical function of angles in degrees, which is multicentred Gaussian-based potentials. So I think it must be some other reasons that cause the issues. Anyway, thanks again for your reply.
Best wishes,
Chaofu Wu, Dr.


From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009 09:39:07 +0200



Hi,

But there could be a very similar issue there for the conversion from radians to degrees.
The force has to be in units of kJ/mol/degree, not kJ/mol/radian.

Berk



From: xiaowu759 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009 15:35:19 +0800



Dear Berk,
   Unfortunately, this time it is angle (table_a0.xvg) that cause the problem. The angles are taken in degrees. I think it is not due to the wrong unit. Anyway, thanks very much for your reply.
 Best wishes,
Chaofu Wu, Dr.


From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009 09:21:18 +0200



Hi,

Last week another user reported very similar problems (also 164% deviations, I think).
In that case it seemed that the user did an Angstrom to nm conversion in the table file
on x without scaling f(x). Could this also be your issue?

Berk



From: xiaowu759 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] a bit strange errors
Date: Fri, 16 Oct 2009 14:55:40 +0800



Dear Mark,
   Thank you very much for the quick reply to my post. According to your suggestion, I check the table and reformat it with equal spacing between entries. I also check the entries calculated from the analytical functions and no wrong values are found. However, the same warnings are given, which lead to terminate the simulation. Are there any other reasons responsible for it?
Best wishes,
Chaofu Wu, Dr. 
> Date: Fri, 16 Oct 2009 14:18:17 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] a bit strange errors
> 
> wuxiao wrote:
> > Dear GMXers,
> > Recently, I has been performing coarse-grained MD simulations based 
> > on the tabulated potentials using GROMACS. In the initialization, some 
> > warnings are given as follows 
> > /WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the 
> > forces deviate on average 164% from minus the numerical derivative of 
> > the potential/
> 
> This looks like your table has either wrong values or wrong formatting.
> It does have to have equal spacing between entries.
> 
> > It proceeds untill at about 17 ns before it is interupted with some errors
> > /WARNING: 1-4 interaction between 148 and 151 at distance 13.125 which > > is larger than the 1-4 table size 2.000 nm/
> > I think the duartion time is long enough to equilibrated the system, 
> > which is confirmed by the energy plot with time. Why it happens so? What 
> > should I do to cope with this problem? Thanks a lot for any reply to 
> 
> Perhaps much of the table is fine, and the problem only arises when you
> get a force being looked up in an erroneous part.
> 
> Mark
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