Dear gmx users, I am trying to equilibrate POPE lipid bilayer. As per mailing list (http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.), C6/C12 parameters are converted into sigma/epsilon. I modified " H " atom type to opls_369 in pope.itp file(show below).
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 opls_369 1 POPE H1 0 0.4000 1.0080 ; qtot:0.36 2 opls_369 1 POPE H2 0 0.4000 1.0080 ; qtot:0.72 3 opls_369 1 POPE H3 0 0.4000 1.0008 ; qtot:1.08 4 LNL 1 POPE N4 0 -0.5000 14.0067 ; qtot:0.76 5 LH2 1 POPE C5 0 0.3000 14.0270 ; qtot:1.0 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I didn't get any error messages while runing "grompp" command. But when runing mdrun commnad, i got the fallowing error. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Step 33, time 0.066 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.037791 (between atoms 6057 and 6105) rms 0.000470 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 6057 6105 90.0 0.1000 0.1038 0.1000 Step 34, time 0.068 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001669 (between atoms 6057 and 6105) rms 0.000025 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 6057 6105 58.4 0.1038 0.1002 0.1000 Step 35, time 0.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.005961 (between atoms 6057 and 6105) rms 0.000082 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 6057 6105 68.1 0.1002 0.0994 0.1000 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx My question is 1) Where I have to modify H atom type given in pope.itp file ( given that "added atomtype H from opls_369 to match H expected by pope.itp" in atomtypes section: http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.) Any suggestion is appreciated. Thank you in advance with best regards, Nagaraju ____________________________________________________________________________________ Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ _______________________________________________ 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