From: Charlie (charlie018_at_yahoo.cn)
Date: Wed Dec 15 2010 - 21:03:17 CST
I'm a newbie. I have some puzzle about cv-smd.
1. If the input of smd must be output of equilibration ? For another way of saying, must we use equi.restart.vel, equi.restart.coord, equi.restart.xsc in smd configure file ? Can I just use equi.restart.coord and set temperature to substitute equi.restart.vel ？
2. When I use equi.restart.vel, the curve of time-distance (between smd atom and fixed atom ) increase suddenly and then slowly, which is far from linear, and set temperature will not encounter this "problem",the curve is nearly linear. I want to know is it a problem.
3. Anybody come across the instance that in the force -extension curve, the force vibrates from negative to positive to negative for a long time. Is this usal or wrong ?
4. Smd need a lot of water , so it's time exhausting. Equilibration need less water and run faster. Can I run a long time of equilibration with little water to get the most probable solutional structure and then change to a larger box .With the protein fixed, let the added water run equilibrate, the do smd ?
Thanks for your attention
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