[gmx-users] LINCS WARNING...

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Jul 30 02:58:01 CEST 2003

>I had tried all-bonds and also tried the SHAKE algorithm earlier. They
>all seem to crash and the culprit always seems to be that one particular
>hydrogen atom. Is there any other way to make it stable?

As suggest by David, I would first look at a nearby 1-4 interaction that is 
too strong.

Another option is to slow down the hydrogen atoms motion by increasing its 
mass by a factor of 4 and then subtracting that "extra" mass off the atom 
it is attached to.  But that isn't likely to help if there is a strong 1-4 
interaction happening that is distorting things too much.

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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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