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

[Payman Pirzadeh]

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?
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)?

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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> 
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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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