Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 during the last minimization , later i solvated the protein using a vanderwaal radii for carbon as 0.375, i found some water molecules not in the core of the lipid layer but to the sides, as they were not in the centre i ionated the complex with 13 chloride ions as the charge shown was non-zero total intergral charge 1.30000e+01, then i minized the ionized complex with the minim.mdp file in as per justin tutorial, i am following all the mdp files as per the tutorial till now, and was able to obtain Potential Energy = -1.8947278e+05 Maximum force = 9.1642163e+02 on atom 7647 Norm of force = 5.0845932e+01
and then i created the index file ane while running the nvt equilllibrqtion i am getting Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.007117, max 0.443345 (between atoms 6311 and 6312) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max 0.068592 (between atoms 6311 and 6312) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 6311 6312 38.8 0.2064 0.1528 0.1430 starting mdrun 'Protein in DPPC in water' 50000 steps, 100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 72506.576935, max 3674667.750000 (between atoms 707 and 711) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2418 2420 35.3 0.1338 0.1935 0.1330 2418 2419 37.3 0.1234 0.1764 0.1230 2414 2416 38.4 0.1532 0.2058 0.1530 ...... ...... and finally a step 0Segmentation fault. Can any body suggest me how to rectify the defect and is it the problem with compliation as i am using gromacs 4.0.3 or the memory space or my running the job. Thanks Ram _______________________________________________ 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
