AMBER Archive (2006)

Subject: AMBER: Problem of QM/MM calculation with amber 9 parallel version

From: Lee Kyung-koo (daum203_at_hanmail.net)
Date: Wed Nov 01 2006 - 13:50:28 CST

Dear Amber users,

I have two question about the QM/MM calculations.

First, I installed Amber 9 to a parallel version.

It's working with multi-process in simulating classical MD.

but in simulating with multi-process in QM/MM calculation, sander are not working.

just runing with one process.

Is it normal?


Next, I want to know about PEPTIDE_CORR option in QM/MM calculation.

I have calculated the system that consist of small QM area(peptide) and remaining MM area.

After some time in simulation, backbone angle(omega angle) was changed to cis form.

Usually, that peptide are not exist in cis form.

To maintain the peptide angle to trans form, I need to use PEPTIDE_CORR option.

I want to know why this phenomenon happen and know papers about this options.

Sincerely, yours


"¿ì¸® ÀÎÅͳÝ, Daum" http://www.daum.net ¡ºÆò»ý¾²´Â ¹«·á ÇѸÞÀϳݡ»
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