[gmx-users] few doubts regarding 1-4 interaction

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 1 05:20:01 CEST 2009

Ms. Aswathy S wrote:
> Thanks Justin.
> I am trying to do the simulation of protein-ligand complex.
> 1. Minimized the protein(but converged before  the Fmax reached the threshold)

What was the target Fmax?  What Fmax did the EM converge to?

> 2. Did a 50 steps of NVT equilibration

50 steps?  That is far too short to be effective.

> 3. Then an NPT equilibration reached at 650 steps (checked the RMSD with the initial structure) 

The NPT script you attached called for 50000 steps.  Did NPT stop prematurely? 
When applying position restraints, RMSD is meaningless as far as whether or not 
equilibration is effective.

> 4. Then tried to do a 3 ns production run. But failed  ~ after 170 ps.
> I am attching the NPT file I have used for equilibration. Also the structure after equilibration does not have any clashes or bad contact in the rough analysis. How can I do a more close checking of this?

You are using Shake to constrain bond lengths.  LINCS is more stable.


> Once again Thank you  for your response.
> Aswathy
> ----- Original Message -----
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Tuesday, June 30, 2009 8:33:19 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] few doubts regarding 1-4 interaction
> Ms. Aswathy S wrote:
>> Hi gromacs users,
>> I am facing the same error during Production run that faced by so many
>> gromacs users and I know this query has been answered for several times. But
>> Could you please tell me some specific doubt regarding the 1-4 interaction
>> error that usually occurs?
>> I have equilibrated my protein ligand system of around 600 ps and shown a
>> satisfied level of equilibration. Then I moved to the Production run of 3ns.
>> But shows the same 1-4 interaction error. My doubts are,
>> 1. It was advised by gromacs experts that better I should go for another
>> round of minimization. Is it on the equilibrated structure?
> It would be good if you could remind us of what you are doing, as well as cite
> the actual post where you were told to do this.
>> 2. If so Do i need to equilibrate again after minimization?
> Yes.
>> 3. I have did 2500 steps of minimization on the structure which is
>> equilibrated and then again run for 3ns production run But occured the same
>> error at 3 lakh step? if I reduce my time step how that will affect this
>> error(I have seen in the error section of gromacs that another possibility is
>> to reduce the time step?)
> Reducing the timestep can in some cases finesse the problem into behaving.  If
> there is something more deeply wrong with your model, then this probably won't
> help out a whole lot.
> If you can post a more complete description of what it is you are doing, what
> parameters you are using, etc. you might get more detailed suggestions.  The
> bottom line is, if your system is blowing up, something about the model physics
> is unreasonable.
> -Justin
>> Can you please tell me your suggestion on these??
>> Thank you. Aswathy
>> Dept. Biotechnology Ext. 3108 _______________________________________________
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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