Modellers:

When setting up an optimization, how does one define a different number of iterations for the conjugate graidents and MD stages?

In one of the scripts provided with the program I see the variable: SET MAX_VAR_ITERATIONS = 500

..which I presume sets the number of iterations for the CG stage - so is there a corresponding variable MAX_??_ITERATIONS for MD stage? or does setting MAX_ITERATIONS set the number of MD iterations?

i.e. will..

SET MAX_VAR_ITERATIONS = 500 SET MAX_ITERATIONS = 1000

..in my modelling script do 500 steps of CG followed by 1000 steps of MD? I see no note of MAX_VAR_ITERATIONS in the Index..

also, is it common to SET MD_RETURN = MINIMAL, or to FINAL? I presume MINIMAL?

Further, in the default _model script is equilibration (INIT_VELOCITIES) set to ON? In the _defs script it is not defined, so is it on by default, and what effect may this have on optimization?

Last, what effect does running the MD stage at high temperatures have on the model? Presumably, more conformational space is sampled, and if the MINIMAL model is chosen, perhaps this may be of lower PDF than if a lower temperature was chosen?

Thanks in advance,

Nick

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Nicholas Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada

Tel: (604) 291-4531 Fax: (604) 291-3765

email: nglover@sfu.ca