[gmx-users] Re: About Error in Equlibration while using CYC pdb
jalemkul at vt.edu
Thu Oct 11 16:38:48 CEST 2012
Please keep the discussion on the mailing list. I have told you several times
that I do not reply to private Gromacs help requests unless I ask you to send me
files for diagnostic purposes. You stand a better chance of resolving the issue
with the help of the community, and the resolution will (hopefully) serve as a
helpful thread for others in the future.
On 10/11/12 10:04 AM, vidhya sankar wrote:
> Dear Justin Thank you for your previous reply For remembrance I have pasted
> Here your previous reply
> You don't necessarily have to use LINCS, but constraints are commonly applied in
> order to use longer timesteps, and rigid bonds are a better model of reality.
> Simple visualization does not indicate that the topology is sound. The fact
> that your EM is insufficient and that the equilibration run fails instantly
> indicates that the starting geometry, topology, or both, are problematic. Based
> on the available information, we can't tell what is the source of the problem.
> I Have attched my Topology and Pdb to your Mail Please Give Possible
> suggestion and pint out error in topology and Pdb
> Gromacs Mailing List Does not allow any Attachemnt so I have sent you to your
> Mail Regret me if you feel inconvenience
I'm not going to hunt through a 1100-line file and hope to figure out what
you've done to try to make it work. You need to describe precisely what
modifications you have made, show any relevant snippets (which can be copied and
pasted, rather than sending attachments).
> then You Gave the HyperLink for Diagonastic steps
> In That page They told me To use g_energy tool. it Quoted that Spiking of
> intramolecular term indicates improper bonded parameter
> What is the Meaning of the Above statement Viz Spiking ?
A spike is a sudden increase.
> Also Which Term Should i select When i run g_energy tool To detect the spiking
> of Intramolcular term either Bonded Parameter or Nonbonded Parameter
Any of the terms may be useful. It's impossible to try to guess which one, if
any, will reveal the source of the problem.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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