<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:12pt"><DIV>I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords-</DIV>
<DIV><FONT size=2>
<P>--------------------------------------------------------;</P>
<P>cpp = /usr/bin/cpp</P>
<P>define = -DFLEX_SPC</P>
<P>constraints = none</P>
<P>integrator = steep</P>
<P>nsteps = 2000</P>
<P>;</P>
<P>; Energy minimizing stuff</P>
<P>;</P>
<P>emtol = 2000</P>
<P>emstep = 0.01</P>
<P>nstcomm = 1</P>
<P>ns_type = grid</P>
<P>rlist = 1</P>
<P>coulombtype = PME</P>
<P>rcoulomb = 1.0</P>
<P>rvdw = 1.0</P>
<P>Tcoupl = no</P>
<P>Pcoupl = no</P>
<P>gen_vel = no</P>
<P>----------------------------------------------------------------------</P>
<P>The output shows</P><FONT size=2>
<P>Steepest Descents converged to Fmax < 2000 in 203 steps</P>
<P>Potential Energy = -5.8639745e+06</P>
<P>Maximum force = 1.7305787e+03 on atom 777</P>
<P>Norm of force = 4.4084099e+01</P>
<P> </P>
<P>But when I am trying the position retraining step, with following keywords in pr.mdp file-</P><FONT size=2>
<P>------------------------------------------------------------</P>
<P>title = Yo</P>
<P>cpp = /usr/bin/cpp</P>
<P>define = -DPOSRES</P>
<P>constraints = all-bonds</P>
<P>integrator = md</P>
<P>dt = 0.002 ; ps !</P>
<P>nsteps = 10000 ; total 20.0 ps.</P>
<P>nstcomm = 1</P>
<P>nstxout = 250</P>
<P>nstvout = 1000</P>
<P>nstfout = 0</P>
<P>nstlog = 10</P>
<P>nstenergy = 10</P>
<P>nstlist = 10</P>
<P>ns_type = grid</P>
<P>rlist = 1.0</P>
<P>coulombtype = PME</P>
<P>rcoulomb = 1.0</P>
<P>rvdw = 1.4</P>
<P>; Berendsen temperature coupling is on </P>
<P>Tcoupl = v-rescale</P>
<P>tc-grps = Protein SOL SF4 </P>
<P>tau_t = 0.1 0.1 0.1</P>
<P>ref_t = 300 300 300 </P>
<P>; Energy monitoring</P>
<P>energygrps = Protein SOL SF4</P>
<P>; Pressure coupling is on</P>
<P>Pcoupl = parrinello-rahman</P>
<P>tau_p = 0.5</P>
<P>compressibility = 4.5e-5</P>
<P>ref_p = 1.0</P>
<P>; Generate velocites is on at 300 K.</P>
<P>gen_vel = yes</P>
<P>gen_temp = 300.0</P>
<P>gen_seed = 173529</P>
<P>----------------------------------------------------------------</P>
<P>an error is generated with LINCS warning----</P><FONT size=2>
<P>Step 155, time 0.31 (ps) LINCS WARNING</P>
<P>relative constraint deviation after LINCS:</P>
<P>rms inf, max 14002532367890120704.000000 (between atoms 5093 and 5096)</P>
<P>bonds that rotated more than 30 degrees:</P>
<P>atom 1 atom 2 angle previous, current, constraint length</P>
<P>1193 1195 40.1 0.1330 0.1913 0.1330</P>
<P>1193 1194 38.7 0.1230 0.1757 0.1230</P>
<P>1191 1192 77.7 0.1530 210.9258 0.1530</P>
<P>1189 1193 63.7 0.1530 193.1889 0.1530</P>
<P>1189 1190 75.9 0.1530 193.1568 0.1530</P>
<P>1188 1192 65.6 0.1470 893.4214 0.1470</P>
<P>1188 1189 67.7 0.1470 909.7200 0.1470</P>
<P>1186 1188 72.8 0.1330 3701.8413 0.1330</P>
<P>1186 1187 78.6 0.1230 3824.8157 0.1230</P>
<P>1184 1185 79.5 0.1780 57.6559 0.1780</P>
<P>1183 1184 79.3 0.1829 539.6799 0.1830</P>
<P>1182 1183 85.5 0.1530 3695.6021 0.1530</P>
<P>1181 1186 84.6 0.1530 14910.0859 0.1530</P>
<P>1181 1182 86.6 0.1530 15403.3672 0.1530</P>
<P>1179 1181 87.4 0.1470 35502.0234 0.1470</P>
<P>1179 1180 89.9 0.1000 1119163.2500 0.1000</P>
<P>1177 1179 86.7 0.1330 37732.0156 0.1330</P>
<P>1177 1178 85.9 0.1230 17608.4004 0.1230</P>
<P>1175 1177 99.6 0.1530 50041.0938 0.1530</P>
<P>1175 1176 102.3 0.1530 37907.5586 0.1530</P>
<P>1173 1175 117.7 0.1470 698413.0625 0.1470</P>
<P>1173 1174 120.6 0.1000 677364.4375 0.1000</P>
<P>1171 1173 107.2 0.1330 4168765.5000 0.1330</P>
<P>1171 1172 108.5 0.1230 4103918.2500 0.1230</P>
<P>1169 1170 112.9 0.1090 9872814.0000 0.1090</P>
<P>1167 1169 92.1 0.1390 68041384.0000 0.1390</P><FONT size=2>
<P>t = 0.310 ps: Water molecule starting at atom 196197 can not be settled.</P>
<P>Check for bad contacts and/or reduce the timestep.</P>
<P>Wrote pdb files with previous and current coordinates</P></FONT>
<P>---------------------------------------------------------------------------------------------</P>
<P> </P>
<P>These atoms 5093 and 5096 are the Iron atoms of the cluster.</P>
<P> </P>
<P><STRONG>Now My question is-</STRONG></P>
<P><STRONG>a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group?</STRONG></P>
<P><STRONG>b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step?</STRONG></P>
<P><STRONG>c) Is there any other alternative to correct the linc warning error?</STRONG></P></FONT></FONT></FONT></FONT></DIV><!-- cg6.c50.mail.in.yahoo.com compressed Mon Dec 14 21:30:03 PST 2009 --></div><br>
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