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

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 7 15:22:53 CEST 2012

On 6/7/12 9:14 AM, xiaowu759 wrote:
> Date: Thu, 07 Jun 2012 07:59:27 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4FD0979F.4020702 at vt.edu <mailto: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

A distance of several hundred nm would indicate to me that the system blew up.

>  >> 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.

That's a 29% difference, which is quite large.  If constraints are not easily 
satisfied, the simulation can blow up.  Your statement above makes that seem 
very likely.  Your restraint distance should match the actual coordinates very 
closely, otherwise you will likely need to equilibrate better under e.g. an 
umbrella potential and relatively weak force constant to obtain better starting 
structures if you're intent on using a rigid constraint for the PMF calculation.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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