[gmx-users] How to set up constraint distcance pulling

[xiaowu759]

Date: Thu, 07 Jun 2012 07:59:27 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] How to set up constraint distcance pulling
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FD0979F.4020702 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Thank you very much!
 
On 6/7/12 7:38 AM, xiaowu759 wrote:
>> Dear gmxers,
>> I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of
>> distance between the COMs of two molecules. However, quite strange resuluts are
>> generated, i.e., the distance can not be fixed at the value defined by
>>pull_init1. The pull opinions are given below. Could you please tell me how to
>> deal with this? Thanks a lot for any reply.

>How far away from the target value are the results in terms of COM distance?
A: very far, several hundreds vs. 0.8 nm
>> Chaofu Wu
>> ;Pull opinions
>> pull = constraint
>> pull_geometry = distance
>> ;pull_dim = Y Y Y

>The comment here has no effect; pull_dim defaults to "Y Y Y."
A: Yes
>> pull_group0 = r1
> >pull_group1 = r2
> >pull_nstxout = 0
> >pull_nstfout = 5
>> pull_init1 = 0.80

>How does this pull_init1 value compare to the COM separation in the coordinate 
>file? If the distance is not very close, the constraint algorithm may fail.
A: The COM separation in the coordinate file is 0.567 nm, which should be not too larger than 0.80 defined by pull_init1. 
>-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
  ------------------
   Department of Chemistry and Materials Science

 Hunan University of Humanities, Science and Technology, 
 Loudi 417000, the People's Republic of China (P.R. China)
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