[gmx-users] [Fwd: questions of afm pulling code]

[David van der Spoel]

-------- Forwarded Message --------
From: Jian Zou <zouj01 at mails.tsinghua.edu.cn>
To: spoel at xray.bmc.uu.se
Subject: questions of afm pulling code
Date: Thu, 9 Dec 2004 22:02:28 +0800
Hi Mr. David van der Spoel,

I tried to use "afm_rate1=0.001" but found the pulling group moved too fast.

I checked the manual but found that the unit for afm_rate is changed from
nm/timestep to nm/ps.
I'm just wondering if nm/ps for afm_rate is a typo in manual 3.2, and some
one in the mailing list also agrees with me.

I checked gmx-3.2.1/src/mdlib/pull.c, and fould
pull->grp[i].spring[m] = pull->grp[i].AfmInit[m] + pull->ref.x_unc[m] +
   pull->grp[i].AfmVec[m]*pull->grp[i].AfmRate*step*dt;
It seems that nm/ps should be correct for gmx 3.2.1.

Therefore I am confused.


Another problem I'm facing is how to set ref_group to be the absolute
coordinate. The manual says that just leave it blank. I did so but error
occured. Is this a bug or I missed something?


Could you please help me with these two questions?

Thanks in advance.


Regards,

Jian Zou
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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