Re: [gmx-users] linc warnings
subarna thakur wrote: Hi, I am using the following keywords in pr.mdp file for the simulation for protein with fe4s4 cluster; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 150; total 3000 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps= ProteinNon-Protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps= Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the Fe4s4 cluster atoms are showing large rms and rotating hugely in position restraining step and Linc warnings are comming. In some published papers it is mentioned that during the molecular dynamics simulations, the proteins' heavy atoms and the counter ions were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? That's what position restraints are doing. Watch the trajectory, and see if you can find where things are going wrong. If the crash is happening reasonably early, you can set nstxout = 1 to get a bunch of frames right before the crash. Perhaps there are some atomic clashes that are still unresolved after EM. The Fmax you achieved before is indeed quite high. Have a look around atom 820 and see where the clash might be. Another possibility for the instability of your system is of course inappropriate parameters in the topology. How have you parameterized the Fe4S4 cluster? MM force fields generally fail spectacularly for such transition metal species, especially with the quantum effects (charge transfer, etc) present in such systems. Have you seen the following? http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species -Justin subarna *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, 29 December, 2009 5:44:03 PM *Subject:* Re: [gmx-users] linc warnings subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force= 1.7402682e+03 on atom 820 Norm of force= 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together If EM worked nicely, then something else you are doing is incorrect. snip the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms.. Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings? Without seeing your .mdp file and perhaps even snippets of your topology pertaining to the Fe4S4 cluster, there's nothing else to say except please read the standard advice: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS
Re: [gmx-users] linc warnings
Justin A. Lemkul wrote: snip were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? That's what position restraints are doing. I should amend this slightly. I assumed your Fe4S4 cluster was simply part of your protein, which is restrained with posre.itp, generated by pdb2gmx. If this is not the case, you will have to use genrestr to generate a position restraint file for the Fe4S4 cluster, if it is indeed a separate molecule type. I doubt that restraining the Fe4S4 cluster will fix anything. Please see my last message - there are clashes in your system or inappropriate parameters at play. If you restrain the atoms, you may be just delaying the inevitable crash. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] linc warnings
Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force = 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together Step 228, time 0.456 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 51159085.131913, max 1100381184.00 (between atoms 5437 and 5444) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1262 1264 38.80.1009 0.1054 0.1000 1262 1263 83.60.1035 0.0960 0.1000 1261 1265 42.10.1349 0.1366 0.1340 1259 1261 42.90.1359 0.1372 0.1340 1237 1241 33.00.1480 0.1788 0.1470 1235 1237 75.60.1360 0.4797 0.1330 1235 1236 40.90.1254 0.3422 0.1230 1232 1233 71.30.1834 0.3421 0.1830 1231 1232 43.10.1559 0.3294 0.1530 1230 1235 106.00.1589 0.2070 0.1530 1230 1231 111.00.1606 0.3819 0.1530 1228 1230 81.90.1535 8.3688 0.1470 1228 1229 100.80.1040 7.2523 0.1000 1226 1228 108.70.1480 29.6051 0.1330 1226 1227 112.00.1271 25.3002 0.1230 1224 1226 67.70.2210 50.5775 0.1530 1224 1225 73.60.2217 43.8606 0.1530 1222 1224 146.53.0118 273.3403 0.1470 1222 1223 173.15.0766 350.6593 0.1000 1220 1222 140.6 50.1464 1239.3472 0.1330 1220 1221 142.5 50.5481 1210.8007 0.1230 1218 1219 46.50.1089 0.0687 0.1090 1216 1218 106.30.1532 2.4558 0.1390 1216 1217 57.30.1434 2.4980 0.1090 1214 1218 106.40.1028 2.6673 0.1390 1214 1215 166.40.2538 2.1798 0.1090 1212 1216 119.00.5844 15.3761 0.1390 1212 1213 50.70.5406 17..8588 0.1090 1210 1214 116.20.9490 16.1642 0.1390 1210 1211 150.40.7387 23.8303 0.1090 1209 1212 57.44.3532 165.6521 0.1390 1209 1210 53.54.3615 166.9433 0.1390 1208 1209 130.9 34.7441 858.7278 0.1530 1207 1220 174.9 199.1050 3552.6362 0.1530 1207 1208 172.1 195.9491 3367.8894 0.1530 1205 1207 176.1 490.9904 5776.2954 0.1470 1205 1206 177.8 631.7326 5326.1118 0.1000 1203 1205 179.0 1242.0747 9168.7764 0.1330 1203 1204 178.9 1057.3107 7388.7915 0.1230 1202 1203 179.3 1221.3862 8532.1836 0.1530 1200 1202 177.8 455.7037 3702.9392 0.1470 1200 1201 172.7 158.7020 1978.1310 0.1000 1198 1200 174.2 160.3432 1536.1411 0.1330 1198 1199 92.0 16.9060 423.7516 0.1230 1197 1198 94.1 16.9010 421.8028 0.1530 1195 1197 99.1 10.3514 9.3388 0.1470 1195 1196 96.29.0920 8.6023 0.1000 1193 1195 91.2 21.5753 58.1620 0..1330 1193 1194 89.2 21.1892 62.7649 0.1230 1191 1192 90.1 50.3829 12.4455 0.1330 1190 1191 89.4 13.1419 10.9133 0.1830 1189 1193 114.3 75.7546 37.4387 0.1530 1189 1190 91.1 24.9488 56.3341 0.1530 1187 1189 146.9 53.8226 42.4679 0.1470 1187 1188 139.0 22.0031 100.4932 0.1000 1185 1187 163.3 21.1472 184.6258 0.1330 1185 1186 170.3 61.0351 169.5860 0.1230 1182 1184 153.34.0050 30.0847 0.1530 1182 1183 109.92.7482 31.3314 0.1530 1181 1185 170.1 69.8200 192.5774 0.1530 1181 1182 129.0 21.4261 109.4787 0.1530 1179 1181 132.8 19.8073 116.5793 0.1470 1179 1180 159.42.3810 48.3401 0..1000 1177 1179 175.21.4786 53.0837 0.1330 1177 1178 166.40.7559 28.5291 0.1230 1174 1176 90.00.1801 80.6845 0.1530 1174 1175 99.70.2091 19.2129 0.1530 1173 1177 149.10.2721 28.0611 0.1530 1173 1174 73.60.7968 36.5323 0.1530 1171 1173 87.80.8744 115.1496 0.1470 1171 1172 91.20.1603 111.8982 0.1000 1169 1171 89.70.2456 106.5120 0.1330 1169 1170 90.00.1499 17.6986 0.1230 1166 1168 76.10.1256 0.4912 0.1250 1166 1167 77.80.1256 0.4782 0.1250 1165 1166 71.90.1546 2.7698 0.1530 1164 1169 83.50.1781 17.7449 0.1530 1164 1165 89.30.1594 8.0829 0..1530 1162 1164 88.00.1531 8.2075 0.1470 1162 1163 75.00.1015 0.7203 0.1000 1160 1162 77.50.1343 1.0789
Re: [gmx-users] linc warnings
subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force = 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together If EM worked nicely, then something else you are doing is incorrect. snip the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms. Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings? Without seeing your .mdp file and perhaps even snippets of your topology pertaining to the Fe4S4 cluster, there's nothing else to say except please read the standard advice: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] linc warnings
Hi, I am using the following keywords in pr.mdp file for the simulation for protein with fe4s4 cluster; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 150; total 3000 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps= ProteinNon-Protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps= Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the Fe4s4 cluster atoms are showing large rms and rotating hugely in position restraining step and Linc warnings are comming. In some published papers it is mentioned that during the molecular dynamics simulations, the proteins' heavy atoms and the counter ions were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? subarna From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, 29 December, 2009 5:44:03 PM Subject: Re: [gmx-users] linc warnings subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force = 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together If EM worked nicely, then something else you are doing is incorrect. snip the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms. Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings? Without seeing your .mdp file and perhaps even snippets of your topology pertaining to the Fe4S4 cluster, there's nothing else to say except please read the standard advice: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-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
