In order to get help you need to help us.
How exactly did you try to rasie the temperature?
What Amber version? What thermostat option?
Did you follow the examples in the tutorials?
You should answer these and also include your input
file.
Yes, restraints should usually be used for equilibration.
This email list is not the place to describe a full
equilibration procedure in detail. Follow the tutorials
or else follow a procedure described in a paper that
gets good results for a system similar to yours. Only
change from the tutorials or papers published in good
journals when you have enough experience to be able
to decide why something should be done differently.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
tonglei wrote:
> hello everyone
> How to control the velocity of raising temprature? When I tell
>"sander" the velocity of raising temprature, for example : temprature
>increase 50K every 5ps, but it didn't follow my command ,especially
>the temprature can't raise to my expect temprature in the previous set
>times (ps).
> When I didn't set the velocity of raising tempratue, the system can
>dramatically from 0K raise to 300K at 14ps. Does this method bring
>unreal changes of protein conformation?
> So I wonder how to control the velocity of raising temprature,
> what's the best one?
> In additon, a smaller restraint force is added on the protein in
>amber tutorial. Is this restraint force neccessary? If neccessary ,
>how about hold this smaller force only onto the Ca backbone atom?
> Thanks in advance
>
>--
> Na Zhang
> Chemistry Department
> Zhejiang University PRC
> xbcdnana.gmail.com
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Received on Mon Nov 21 2005 - 13:53:00 PST
