[gmx-users] g_rms problem

Dmitry Kovalsky dikov at imbg.org.ua
Wed Sep 17 14:08:01 CEST 2003


I want to use g_rms to compare a final conformation to an initial one by 
computing rmsd of their  Ca atoms. It gives me a value of 3A. Visual 
comparision tells me that this value is too high. I used DeepView to do it 
again and it gives me a value of 1.6A, which is reasonable. Why g_rms gives 
high values or tell me what I'm doing wrong.

Sincerely yours,

Ph.D. Student Dmytro Kovalskyy
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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