Hello. I am currently using GROMACS4.6.5 and trying to simulate a fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme part(res#1002-1161), so I removed it to make the simulation consistent with our experimental data. As a result, there is a gap in M2 structure, which means M2 is divided into two chains(res#20-217, res#377-456), and when in NVT equilibration process, these chains move apart from each other because both are positively charged. I would like to keep the conformation of M2 and immobilize it in simulation to see only the motion of the fluorescent protein, so I applied position restrains to M2, but two chains still move away from each other and eventually I get many LINCS warnings during NVT equilibration process and simulation collapses.
My question is: Position restrain is a proper way to keep conformations of proteins which have the same charge? Or is there any other way to do so? I am using all-bonds constraint and 2fs time step to save the simulation time. Other fundamental parameters are default. Any help would be appreciated. Thank you very much. Koki Below is the error messages during NVT equilibration process: ----------------------------------------------------------------------- relative constraint deviation after LINCS: rms 0.050664, max 3.739141 (between atoms 962 and 963) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 962 963 89.9 0.1109 0.5118 0.1080 964 965 90.1 0.1106 0.4336 0.1111 964 966 31.9 0.1104 0.1199 0.1111 Wrote pdb files with previous and current coordinates Step 575382, time 575.382 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 611.466194, max 51433.625000 (between atoms 570 and 573) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 555 557 46.2 0.1345 0.1917 0.1345 557 558 49.3 0.0997 0.1394 0.0997 557 559 82.2 0.1430 0.4301 0.1430 559 560 78.3 0.1080 0.3101 0.1080 559 561 84.3 0.1538 1.6306 0.1538 559 574 80.8 0.1490 0.3913 0.1490 561 562 85.8 0.1111 1.4345 0.1111 561 563 85.0 0.1111 1.3860 0.1111 561 564 88.6 0.1538 7.0559 0.1538 564 565 88.3 0.1111 6.1646 0.1111 564 566 88.8 0.1538 6.5956 0.1538 564 570 145.8 0.1538 18.8304 0.1538 566 567 87.6 0.1111 1.7574 0.1111 566 568 87.6 0.1111 1.7576 0.1111 566 569 88.0 0.1111 1.7916 0.1111 570 571 90.0 0.1111 10.2121 0.1111 570 572 125.4 0.1111 10.2996 0.1111 570 573 90.0 0.1111 5714.3872 0.1111 574 575 42.6 0.1230 0.1646 0.1230 574 576 42.1 0.1345 0.1834 0.1345 916 917 33.8 0.0997 0.1182 0.0997 916 918 115.0 0.1428 2.7045 0.1430 918 919 92.6 0.1079 2.7119 0.1080 918 920 149.6 0.1533 2.6632 0.1538 920 921 36.5 0.1111 0.1355 0.1111 920 922 35.7 0.1111 0.1401 0.1111 933 934 106.0 0.1226 2.8814 0.1230 933 960 86.3 0.1372 9.0101 0.1345 935 962 121.3 0.1295 70.4373 0.1490 936 940 172.6 0.1365 9.4523 0.1400 937 955 150.4 0.1411 9.9921 0.1450 938 939 43.2 0.1241 4.6305 0.1220 938 940 79.6 0.1482 1.2946 0.1490 940 941 48.9 0.1378 3.7713 0.1360 941 942 42.8 0.1098 0.1650 0.1100 941 943 33.2 0.1444 0.2096 0.1450 955 956 73.3 0.1086 4.4738 0.1080 955 957 68.8 0.1085 3.8836 0.1080 955 958 43.4 0.1509 4.5246 0.1490 958 959 33.6 0.1226 0.1674 0.1230 958 969 36.3 0.1343 0.1844 0.1345 962 963 103.5 0.5118 19.1058 0.1080 962 964 131.9 0.1441 141.6376 0.1538 964 965 88.9 0.4336 2773.4438 0.1111 964 966 58.9 0.1199 82.5709 0.1111 964 967 55.1 0.1502 133.7226 0.1420 967 968 105.8 0.0947 47.8773 0.0960 Wrote pdb files with previous and current coordinates WARNING: Listed nonbonded interaction between particles 557 and 564 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. ---------------------------------------------------------------------------------- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.