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

[Justin A. Lemkul]

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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