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: xiaowu...@hotmail.com
To: gmx-users@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.abra...@anu.edu.au
> To: gmx-users@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
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
                                          
使用新一代 Windows Liv
 e Messenger 轻松交流和共享! 立刻下载!                                       
_________________________________________________________________
What can you do with the new Windows Live? Find out
http://www.microsoft.com/windows/windowslive/default.aspx
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to