What is the proper value of TMDk in TMD simulations?

From: 常姗燕 (changshanyan_1_at_yahoo.cn)
Date: Sun Oct 23 2011 - 23:21:19 CDT

Dear all,
 
I'm now using TMD to study the conformational transition of a membrane protein. The number of targeted atoms is about 1200. The value of TMDFinalRMSD is 0. 
 
I've found that during the simulations, RMSD fails to keep pace with the target value:
1)  If the TMDk is 580 (i.e. 0.5 for each atom), the RMSD in the end of the simulation is 2.06 Å;
2)  If the TMDk is 5800 (i.e. 5 for each atom), the RMSD in the end of the simulation is 0.7 Å;
 
The user guide says that 'A value of 200 seems to work well in many cases'. Compared to that, my value of 5800 seems too large.
1)  What is the proper value of TMDk? Do the values of TMDk have upper limit?
2)  How can I know that my TMD simulations are right or wrong?
 
Best wishes,
Chang Shanyan
Graduate student of Biochemical Engineering,
TJU, China

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