[gmx-users] Energy Minimization problem

Venky Krishna venky.agas at gmail.com
Thu Apr 19 03:45:35 CEST 2007

Hi George,

I usually delete/move the molecules reported to have high force  
values in the minimization steps. A better thing would be to start  
with a box which has sufficient intermolecular distance again by  
deleting molecules which are very close to each other (use the  
g_mindist program) and then energy minimize the system. Btw...did you  
define FLEXIBLE for water molecules during your em runs?


On Apr 18, 2007, at 5:24 PM, George Abadir wrote:

> Hi,
>      I am doing an energy minimization for a carbon nanotube (end  
> capped with hydrogen atoms) in a box of water. I get the following  
> message:
> " Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision  Fmax < 10
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn off  
> constraints altogether (set constraints = none in mdp file)
> Steepest Descents converged to machine precision in 1836 steps, but  
> did not reach the requested Fmax < 10.
> Potential Energy = -2.4277438+06
> Maximum force = 5.9858018+03  on atom 13
> Norm of force =  5.1364398+04"
> The potential energy is extremely low and the maximum force is  
> considerably large. I turned off the constrained and tried other  
> energy minimization methods but still got the same error (with  
> different magnitudes of the force and energy of course). Is it  
> likely that double precision simulation can make such a big  
> difference? If not (which I think) is there any other way to solve  
> the problem?
> Thank you very much in advance,
> George Abadir
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070418/3cbb7c54/attachment.html>

More information about the gromacs.org_gmx-users mailing list