Dear colleagues,
I thank Justin for your suggesting me the distance
restraints.So, if I want to impose a distance restraint for 11.28 A between two
atoms 4811 and 4812, I would include the following lines in the topology file.
[distance_restraints]
;ai aj type index type' low up1 up2 fac
4811 4812 1 0 1 11.28 11.38 11.48 1.0
I am skeptical about low, up1 and up2 values. I used 11.28 as value for low, as
this is the distance I want the the two atoms be far off. Up1 and up2 values, I
added randomly 0.1 and 0.2 respectively to the low value. Let me know, if I am
correct.
regards,
Prema.
Date: Thu, 14 Aug 2008 18:43:54 -0400
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Imposing distance restraints between two
residues
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Maybe you would be more interested in a distance *restraint*? Note that
constraints and restraints mean different things in Gromacs. The relevant
manual section is 4.3, with a specific example of how to use distance
restraints
on p. 61.
-Justin
[EMAIL PROTECTED] wrote:
> Dear colleagues,
>
> I want to impose simple distance constraint between the two
> ends of the same protein with missing residues in between. As I went
> through the manual I found I can use "constraints type 2" fixes the
> distance without connecting atoms by a chemical bond.
>
> Manual shows this example for O-H and H-H distances
>
> [ settles ]
>
> ; OW funct doh dhh
>
> 1 1 0.1 0.16333
>
> [ exclusions ]
>
> 1 2 3
>
> 2 1 3
>
> 3 1 2
>
> How can I do this for e.g. between two CA of the residues. Also, do
> you suggest SHAKE or LINCS for this purpose? If you can give an example
> for residues, just like the one above for water, that would be great.
> Thanks in advance for any kind of suggestion in this regard.
>
>
> warm regards,
> Prema,
> Graduate student,
> UOH.
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