[gmx-users] about md simulation

[chiradip chatterjee]

Hi Amrita,
I have faced similar problem.....before MD run, try to
minimize water box and protein seperately with both CG
and SD, then put protein in the water box and minimize
it again .., then go for MD run, I think after that
you dont have any Lincs warning..
Chiradip


--- amri ta <amrita0092002 at yahoo.co.in> wrote:

> Dear colleagues,
> I am simulating a phosphorylated protein embedded in
> waterbox. When I try running mdrun, I get a LINCS
> warning.
> Does this mean that I have go back to the CG-EM step
> and use the double 
> precision libs?
> The md.log file reads:
> 
> Initializing LINear Constraint Solver
>   number of constraints is 2365
>   average number of constraints coupled to one
> constraint is 2.5
> 
>    Rel. Constraint Deviation:  Max    between atoms 
>    RMS
>        Before LINCS         0.336565   691       696
>   0.033770
>         After LINCS         0.342830    698       
> 700   0.028042
> 
> Step -1, time -0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.858278 (between atoms 3397 and 3398) rms
> 0.016634
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint
> length
>    3395   3398   76.2    0.1341   0.0446      0.1470
>    3398   3399   78.8    0.1341   0.0492      0.1470
> Constraint error in algorithm Lincs at step -1
> Grid: 10 x 10 x 10 cells
> Configuring nonbonded kernels....
> Testing x86_64 SSE supports...presents
>            
>    Rel. Constraint Deviation:  Max    between atoms 
>    RMS
>        Before LINCS         70.089874   1537   1456 
>  0.559021
>         After LINCS         29.983810   3223   3224 
>   0.787549
> 
> Like this, errors showed "Constraint error in
> algorithm Lincs at step 0, step1" and the simulation
> stops at step 1. Do I have to modify my md.mdp to
> remedy this?
> Your advice is appreciated.
>  Best regards,
> 
> Amrita Ghosh
> National Institute of Mental Health and
> Neurosciences,
> Bangalore-29.
> India.
> 
> 
>       5, 50, 500, 5000 - Store N number of mails in
> your inbox. Go to
http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html>
_______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


Chiradip Chatterjee 
Senior research fellow
Structural Biology Division
Department of Biological Science
National University of Singapore 

Phone:65-92301295
E-mail:chiradip75 at yahoo.co.uk 
       dbscc at nus.edu.sg 
Home Page: www.chem.ucsb.edu/~cchatterjee/ 
I LOVE KOLKATA


      ___________________________________________________________ 
Want ideas for reducing your carbon footprint? Visit Yahoo! For Good  http://uk.promotions.yahoo.com/forgood/environment.html