Re: AMBER: Sander minimization & dynamic question

From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>
Date: Mon, 4 Apr 2005 14:01:32 +0200 (CEST)

Hi,  
I can't comment on most of your points, but you might find the following
article interesting:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15692739
 
>  
> 1. With explicit solvent, the dynamic can only be at room temperature. Am I correct?(http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm)
....You can run dynamics at any temperature (just reduce the timestep for
tempertures significantly above room temp.). However, water models (like
e.g. TIP3P) are most probably optimized to "work best" at room
temperature, but this should not hurt for structure refinement (?).
Of course, your water might not freeze at 273K or start boiling at 373K.

Take the above with a grain of salt,
good luck
Andreas 


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Received on Mon Apr 04 2005 - 13:53:01 PDT
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