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

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 9 15:17:23 CET 2004

-------- 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] +
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.


Jian Zou
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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