Please keep all Gromacs-related correspondence on the gmx-users list. You are far more likely to reach someone with helpful ideas if you send your question out to everyone, and the thread will be archived for others to benefit from in the future. Also, search this archive thoroughly for potential solutions to your problem. There are dozens of posts related specifically to LINCS warnings with membranes.
For information about what a LINCS warning means, refer to the wiki: http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings Probably your EM step did not resolve all bad contacts present in your system. Also, your .mdp file has a problem - never couple solvent and ions to different temperature coupling groups! This may or may not be part of your problem, but is likely to cause headaches at some point. Refer here: http://wiki.gromacs.org/index.php/thermostats In the absence of any other information (how you prepared your system, what you have tried to do to resolve this issue), I can't comment further. Hopefully some of this information is useful. -Justin Quoting ÄÇÃÀÈÙ <[EMAIL PROTECTED]>: > Dear Justin, > I am simulating a system with 5 peptide and a POPC membrane with gromacs . > I > have ran em succefully.But when I ran pr ,I got a LINCS warning: > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 163.380417 (between atoms 25353 and 25354) rms 3.650424 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 25030 25038 34.0 0.1531 0.2013 0.1530 > 25038 25039 40.2 0.1231 0.1764 0.1230 > 25038 25040 71.3 0.1332 0.2284 0.1330 > 25040 25041 73.8 0.1001 0.1599 0.1000 > 25040 25042 80.5 0.1473 0.8682 0.1470 > 25042 25043 78.5 0.1542 2.2823 0.1530 > 25042 25055 80.1 0.1532 0.7523 0.1530 > 25043 25044 83.0 0.1539 5.5148 0.1530 > 25044 25045 80.8 0.1400 4.4305 0.1390 > 25044 25047 87.1 0.1399 17.3262 0.1390 > 25045 25046 71.4 0.1086 1.0713 0.1080 > 25047 25048 88.4 0.1087 14.2386 0.1080 > 25047 25051 88.2 0.1395 12.5692 0.1390 > 25049 25050 75.3 0.1083 1.1422 0.1080 > 25049 25053 85.5 0.1393 3.1301 0.1390 > 25051 25052 86.7 0.1082 6.8091 0.1080 > 25051 25053 85.9 0.1393 5.9519 0.1390 > 25053 25054 86.3 0.1082 3.6976 0.1080 > 25055 25056 71.8 0.1231 0.1754 0.1230 > 25055 25057 65.8 0.1331 0.2104 0.1330 > 25057 25058 39.9 0.1000 0.1405 0.1000 > 25057 25059 36.1 0.1470 0.1931 0.1470 > 25349 25350 78.9 0.1536 1.6355 0.1530 > 25350 25351 163.3 0.1604 1.8178 0.1530 > 25351 25352 43.4 0.1599 5.4292 0.1530 > 25352 25353 97.7 0.1578 24.5403 0.1530 > 25353 25354 83.2 0.1540 24.1639 0.1470 > 25354 25355 109.9 0.1098 3.5962 0.1000 > 25354 25356 108.3 0.1098 3.7714 0.1000 > 25354 25357 93.3 0.1098 5.5208 0.1000 > Constraint error in algorithm Lincs at step 0 > Energies (kJ/mol) > Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14 > 1.45008e+04 6.21453e+03 3.41089e+03 1.62397e+03 5.10741e+03 > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. > 2.74078e+04 5.90825e+06 -4.65849e+03 -1.40426e-05 -1.04918e+07 > Position Rest. Potential Kinetic En. Total Energy Temperature > 2.32371e+01 -4.52991e+06 3.69314e+09 3.68861e+09 1.66285e+07 > Pressure (bar) > 9.25953e+07 > > > Step 1 Warning: pressure scaling more than 1%, mu: 3.77786 3.77786 3.77786 > > Step 1, time 0.001 (ps) LINCS WARNING > relative constraint deviation after LINCS: > .................... > My popc_5ggn_pr.mdp and popc_5ggn.top are attacted below.I don't know where > is > wrong.Your advice is appreciated. Thank you very much. > > Best regards. > wumin > china HuaZhong Normol University > > > > > ======================================== 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
