Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all , > I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from > archives and the link is > *http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html* > The steps I have done are > 1. I added "atom types" from lipid.itp to ffoplsaanb.itp here I got no > exponential values for "sigma" and positive exponential "epsilon" values > when substituted in equations. > (atom types) > ;name name charge mass charge ptype sigma epsilon > LO LO 1 15.9994 0.000 A 0.00011209814 > 2.90868792E+17;carbonyl O, OPLS
I think you have done your calculations wrong. Check the formulas again provided in Chris' post. For example, if I calculate sigma and epsilon according to his equation, I get: sigma = 0.2959999302 epsilon = 0.8786943396 which seem much more reasonable, given the magnitudes of sigma and epsilon from ffoplsaanb.itp. -Justin > > 2. I added "pair types" from lipid.itp to ffoplsaanb.itp same kind of > values came for sigma and epsilon > [ pairtypes ] > ; i j func sigma epsilon > LO LO 1 0.000112183829 3.61555415E+16 > > 3. I added dihedral types from lipid.itp to ffoplsaabon.itp > > LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495 > > 4. Changed OW to opls_116 in ffoplsaa.itp file > 5. Removed HW in ffoplsaa.itp file > > 6. I made toplogy like this > > #include "ffoplsaa.itp" > #include "popc.itp" > #include "spc.itp" > > (sytem name) > (molecules) > protein 1 > POPC 87 > Sol 2020 > all these .itp files included in protein.top file generated by pdb2gmx > command in which took OPLS-FF > > 7.Later ran minimisation it went fine wihtout error > 8. when I am trying to run equilibration, crashed and showed segmentation > fault > The commands used are : grompp -f pr.mdp -c em.gro -p .top -o out.tpr > mdrun -v -deffnm out > > Step 21, time 0.042 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 8904.457031 (between atoms 1124 and 1126) rms 126.620766 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 1120 1121 96.2 0.1470 0.5591 0.1470 > 1121 1122 92.1 0.1530 5.3756 0.1530 > 1122 1123 90.5 0.1430 41.4380 0.1430 > 1123 1124 90.3 0.1610 235.0883 0.1610 > 1124 1125 91.1 0.1480 190.6947 0.1480 > segmentation fault. > > I have 3 doubts > 1.The steps I followed is correct? any comments will be appreciated > 2. No need to include nonbandparameters and parameters for lipid and gromos > interactions from lipid.itp to ffoplsaa.itp ? > 3. LO HW 1 0.00000e+00 0.00000e+00 in this line how we will remove > only HW without changing LO ? > Pls suggest me detail explanation > All comments will be appreciated > Thanks in advance. > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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