[gmx-users] use of DPOSRES without pdb2gmx

[pbuscemi at q.com]

Justin,
Thanks,
Bartimaeus

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Lemkul
Sent: Thursday, January 17, 2019 2:44 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] use of DPOSRES without pdb2gmx



On 1/17/19 3:33 PM, pbuscemi at q.com wrote:
> Dear Users,
>
> Suppose you do not use pdb2gmx  and therefore do not use  the -I 
> option for all constraints. Suppose further you do not generate a 
> restraint file for the non-protein molecules in the model.
>
> Then what effect, if any,  does setting constraints = all-bonds or 
> h-bonds have ?

Constraints and restraints are totally different. If you tell mdrun to
constrain bonds, it will do precisely what you tell it.

-Justin

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Justin A. Lemkul, Ph.D.
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