On 5/18/15 7:53 AM, Ming Tang wrote:
Hi Justin,
Do you mean options for bonds or something like fix and pull atoms?
From the error...
"Maybe you forgot to change the constraints mdp option."
-Justin
-----Original Message-----
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: Monday, 18 May 2015 9:44 PM
To: gmx-us...@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
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Justin A. Lemkul, Ph.D.
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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