[gmx-users] Some parameters in the mdp file

[Mark Abraham]

qiwenpeng at sinap.ac.cn wrote:
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Wednesday, February 08, 2006 8:49 PM
> Subject: Re: [gmx-users] Some parameters in the mdp file
> 
> 
> 
>>qiwenpeng at sinap.ac.cn wrote:
>>
>>>Dear all,
>>> 
>>>I don't use constraints, so I set constraints : none.
>>> 
>>>Under this condition the parameter "unconstrained start" can work or not 
>>>? Does it apply constraints on the system in the beginning when it is 
>>>set no.
>>> 
>>
>>this is irrelevant unless you have settles.
> 
> You mean if  I use constraints = none, no mater yes or no I set for the "unconstrained start"
> 
> There will be no constraints added to the start conformation, right?

Constraints given in the topology are applied after geometries change, 
or at the start of runs. If you are doing a multi-stage MD simulation 
run, you don't want to apply a constraint after the final step in stage 
1, and then re-apply it before the first step in stage 2. This is the 
purpose of stipulating an unconstrained start. If you have no 
constraints set in your topology (including in the solvent, hence 
David's comment about SETTLE) then the setting you mention is irrelevant.

Mark