[gmx-users] EM in vacuum

[Dallas Warren]

>I am trying to prepare the structure for MD run in vacuum and use steep 
>algorithm. But the EM calculation repeatedly ends with
>'did not converge' message. What do you offer for this situation?

That is not necessarily an issue.  What has the forces and energy of the 
system done?  In my experience, with a substantial amount of water in the 
box energies of <10^-4 are sufficient for things to go smoothly.  For the 
limited number of cases where I have done it with no water present, even 
values of the order of 10^4 are fine.  It just depends on what the 
molecules are made up of.

Whether it converges or not depends on the tolerance that you set for 
it.  If the tolerance is too tight, then it wont reach it.  When you move 
to the next stage you will soon tell if the energy minimisation is 
sufficient or not.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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