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@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
