[gmx-users] first residue in chains warning issue

Ming Tang m21.tang at qut.edu.au
Fri May 22 09:39:34 CEST 2015

Dear Justin,

Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints?
If the difference is quite small, then I can choose constraining bonds to increase time step.

Thanks a lot.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Monday, 18 May 2015 9:44 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue

On 5/18/15 7:39 AM, Ming Tang wrote:
> Dear Justin,
> After minimization, I got the following note when using NPT.
> NOTE 1 [file topol.top, line 49]:
>    The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10
>    times the time step of 1.0e-03 ps.  Maybe you forgot to change the constraints mdp option.
> Does this has something to do with the warning given by pdb2gmx?
> When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top?

No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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