> Dear gmx users, > I am thankful to Dr.Mark and Dr.Osmair for > their responce to my queries. As per their suggestion, > I checked ions.itp file in that sodium atoms are > represented by NA+ in opls force field. I am using > gromacs 3.3.1 version.
> zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz > > Step 32, time 0.064 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.002582 (between atoms 5262 and 5310) rms > 0.000038 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length > 5262 5310 31.2 0.1000 0.0997 0.1000 > > Step 33, time 0.066 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.003343 (between atoms 5262 and 5310) rms > 0.000057 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length > 5368 5416 69.4 0.0999 0.1001 0.1000 > > Step 34, time 0.068 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.005428 (between atoms 5262 and 5310) rms > 0.000076 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length > 5262 5310 67.9 0.1003 0.0995 0.1000 > 5368 5416 47.0 0.1001 0.1002 0.1000 > > Step 35, time 0.07 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 0.002371 (between atoms 5368 and 5416) rms > 0.000036 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint > length > 5262 5310 43.4 0.0995 0.1002 0.1000 > 5368 5416 40.9 0.1002 0.0998 0.1000 > zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz > > Can you tell where I have done mistake. > Any suggestion is appreciated. Please read http://wiki.gromacs.org/index.php/Blowing_Up and check that you've followed the advice here http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark _______________________________________________ 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
