[gmx-users] Re: a naive question on restraints and constraints

[Tsjerk Wassenaar]

Hi,

It's actually a bit more nuanced and the use of these idioms is not
really backed by a semantic distinction: In Gromacs, a constraint
fixes some property to a value, whereas a restraint penalizes
deviation of a property from a certain value.

Cheers,

Tsjerk

On Wed, Sep 30, 2009 at 2:03 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Payman Pirzadeh wrote:
>>
>> Hi,    I read the wiki and manual on constraint and restraints, and I am
>> still a
>> bit confused. But, my question is, should I remove the restraints after
>> equilibration in production phase?
>
> A restraint fixes the position of an atom, or the value of an angle,
> dihedral, etc.  So, if you'd like your molecule of interest to actually do
> something during data collection, yes, remove restraints :)
>
>> What about constraints? How should I know my system really needs either of
>> them (is there a general rule or protocol to follow)? If I apply them
>> incorrectly, how will them affect my results (in my case protein)?
>>
>
> A constraint fixes a bond length.  If you don't use constraints, you must
> use a very small dt, like 0.5 fs.  Use of constraints allows you to use a dt
> of 1-2 fs (or more if using virtual sites).  The LINCS papers (cited in the
> manual) describe the background of these methods.  If you apply constraints
> incorrectly (i.e., by not using them and then implementing dt of 2 fs), your
> system will either rapidly collapse, or your total energy will not be
> conserved.
>
> -Justin
>
>> Payman
>>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of Justin A. Lemkul
>> Sent: September 17, 2009 5:38 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] merging simulation boxes
>>
>>
>>
>> Paymon Pirzadeh wrote:
>>>
>>> I have a box of crystal (from another simulation) and a box of solvated
>>> protein. Now I want to put the protein close to my crystal.
>>>
>>
>> Use editconf to define a box for your new system, use -center on each
>> component as appropriate, and cat the two .gro files together (removing
>> the duplicate
>> box info, etc that will be placed in the middle of the new file).
>>
>> -Justin
>>
>>> Payman
>>>
>>>
>>>
>>>
>>> On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote:
>>>>
>>>> Paymon Pirzadeh wrote:
>>>>>
>>>>> Hello,
>>>>> Are there any links on how we can merge two simulation boxes to make a
>>>>> single configuration? What technicalities should be considered?
>>>>
>>>> Define "merge". There's a whole pile of issues depending what you mean.
>>>>
>>>> Why can't you build initial coordinates up from scratch, rather than
>>>> "merge" some pre-existing sets?
>>>>
>>>> Mark
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623