Have a loolk at http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Chadnan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, May 13, 2010 at 10:34 AM, manjula kasinathan <manju...@gmail.com>wrote: > > Hi all > > i have done protein protein interaction and the complex structure > was taken for MD simulation using Gromacs. the length of the protein was > around 1100 aa. while performing mdrun step for position restrain i got > error. i have carried out mdrun for 1ps and the command given for mdrun and > position restrain are > > grompp -f *.pdb -c *.gro -p top.top -o *.tpr > > mdrun -v -deffnm pr > > error i got was > > starting mdrun '? in water' > 500 steps, 1.0 ps. > step 400, remaining runtime: 133 s > Step 416, time 0.832 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000577, max 0.008379 (between atoms 5530 and 5532) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 8190 8191 30.7 0.1014 0.1000 0.1000 > > Step 419, time 0.838 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000874, max 0.019432 (between atoms 5526 and 5527) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 112 113 31.0 0.1017 0.1002 0.1000 > > Step 430, time 0.86 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 158552932798158.562500, max 14888250728513536.000000 (between atoms > 1734 and 1735) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 4469 4471 66.7 0.1327 0.5535 0.1330 > 4469 4470 69.6 0.1227 0.5336 0.1230 > > 8001 8003 47.0 0.0999 0.0998 0.1000 > 7995 7996 30.0 0.1001 0.0999 0.1000 > 7970 7971 34.0 0.0999 0.1002 0.1000 > > t = 0.860 ps: Water molecule starting at atom 81142 can not be settled. > Check for bad contacts and/or reduce the timestep. > Wrote pdb files with previous and current coordinates > > > could any one pls help me to overcome this problem.how give me some ideas. > > looking forward for a solution. thanx in advance. > > > > > > -- > With Regards, > > Manjulakasinathan > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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