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 <[EMAIL PROTECTED]> 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@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 Chiradip Chatterjee Senior research fellow Structural Biology Division Department of Biological Science National University of Singapore Phone:65-92301295 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] 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 _______________________________________________ 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