[gmx-users] error during energy minimization

[Itamar Kass]

On Feb 22, 2005, at 12:07 PM, shailza singh wrote:

>
> Dear Itamar,
> I have one query... i am doing energy minimization of
> the peptide in solvent..for that I followed the steps
> as that given in getting-started Peptide in the
> GROMACS  online reference.The em.mdp file (sample file
> given in the online reference) has integrator as md
> ...do I need to change it as cg?What I did was first
> perform energy minimization of the peptide in
> solvent..then short MD run and finally full MD run.Am
> I proceeding in the right direction?or Do i need to
> change the integator as cg?
>

Hi shailza, the steps you stated seems fine to me, but I am working on 
in membrane peptide. Any how, in order to do EM you should use cg 
integrator.  For example:
define              =  -DFLEX_SPC
integrator           =  cg
nsteps               =  50000
;       Energy minimizing stuff
emtol                =  500.0
emstep               =  0.001

Later on, you should do short MD run in which the peptide atoms are 
restrained, for example:
integrator           =  md
dt                   =  0.002	; ps !
nsteps               =  250000	; total 0.5s.
; Constrain control
define               = -DPOSRES
constraints          = all-bonds
The flag -DPOSRES indicate you use the position restrains given in the 
itp file (e.g. posre_A.itp) created by pdb2gmx.  Later on run a longer 
simulation without position restrains.

> My second question is :I changed both the temperature
> coupling and pressure coupling ...and I got
> step 960, will finish at Tue Feb 22 16:46:00
> 2005Warning: 1-4 interaction between 1528 and 1533 at
> distance larger than 1 nm
> These are ignored for the rest of the simulation
> turn on -debug for more information
>
> Step 961, time 1.922 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.019805 (between atoms 1531 and 1532) rms
> 0.000548
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    1531   1532   51.8    0.9733   0.0980      0.1000
>
> Step 962, time 1.924 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 3.965767 (between atoms 1531 and 1532) rms
> 0.106540
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    1531   1532   90.0    0.0980   0.4966      0.1000
>    1531   1533   90.0    0.0996   0.4604      0.1000
> After this its running fine.
> Please tell me as to where am i doing wrong?
> thanking you in advance
> shailza.
>

This is probably due to some defect in your starting structure, maybe a 
collision between atoms or like.  If it ends fine it O.K..  Again, what 
you did was MD and not EM, I guess that doing EM first will prevent 
this kind of problems.


      Good luck, Itamar.


===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: 
http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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