[gmx-users] Re: About Error in Equlibration while using CYC pdb

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list