<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear gmx users:</DIV>
<DIV> I have read a paper"Atomistic simulation of ion solvation in water explains surface preference of halides", I think it is a perfect work. And I am also interested in the electrolyte behavior at interface. I am using SWM4-NDP polarizable water model and ion Polarizable Alkali and Halide Ions in conjuction with SWM4-NDP water model by GMX4.5.4, I find the RMS force is very large, and at last the system blow up. BUT I simulate pure water with SWM4-NDP water model , It seems everything is OK.<SPAN style="FONT-SIZE: 16px">I need your help, thanks in advance.<BR> Best wishes!<BR> Zhongjin He<BR>The error:<BR>step 177: EM did not converge in 20 iterations, RMS force 0.032<BR>step 178:
EM did not converge in 20 iterations, RMS force 0.033<BR>step 179: EM did not converge in 20 iterations, RMS force 0.033<BR>step 180: EM did not converge in 20 iterations, RMS force 0.033<BR>step 181: EM did not converge in 20 iterations, RMS force 0.032<BR>step 182: EM did not converge in 20 iterations, RMS force 0.033<BR>step 183: EM did not converge in 20 iterations, RMS force 0.033<BR>step 184: EM did not converge in 20 iterations, RMS force 0.033<BR>step 185: EM did not converge in 20 iterations, RMS force 0.032<BR>step 186: EM did not converge in 20 iterations, RMS force 0.033<BR>step 187: EM did not converge in 20 iterations, RMS force 0.032<BR>step 188: EM did not converge in 20 iterations, RMS force 0.033<BR>step 189: EM did not converge in 20 iterations, RMS force 0.033<BR>step 190: EM did not converge in 20 iterations, RMS force 0.032<BR>step 191: EM did not converge in 20 iterations, RMS force 0.033<BR>step 192: EM did not converge in 20
iterations, RMS force 0.033<BR>step 193: EM did not converge in 20 iterations, RMS force 0.033<BR>step 194: EM did not converge in 20 iterations, RMS force 0.035<BR>step 195: EM did not converge in 20 iterations, RMS force 0.042<BR>step 196: EM did not converge in 20 iterations, RMS force 1.898<BR>step 197: EM did not converge in 20 iterations, RMS force 49.403<BR>step 198: EM did not converge in 20 iterations, RMS force 173.436<BR>step 199: EM did not converge in 20 iterations, RMS force 363.106<BR>step 200: EM did not converge in 20 iterations, RMS force 589.073<BR>step 201: EM did not converge in 20 iterations, RMS force 786.105<BR>step 202: EM did not converge in 20 iterations, RMS force 845.617<BR>step 203: EM did not converge in 20 iterations, RMS force 773.659<BR>step 204: EM did not converge in 20 iterations, RMS force 741.854<BR>step 205: EM did not converge in 20 iterations, RMS force 778.916<BR>step 206: EM did not converge in 20 iterations,
RMS force 964.226<BR>step 207: EM did not converge in 20 iterations, RMS force 1340.912<BR>step 208: EM did not converge in 20 iterations, RMS force 1790.702<BR>step 209: EM did not converge in 20 iterations, RMS force 488.729<BR>step 210: EM did not converge in 20 iterations, RMS force 820.419<BR>step 211: EM did not converge in 20 iterations, RMS force 977.581<BR>step 212: EM did not converge in 20 iterations, RMS force 923.088<BR>step 213: EM did not converge in 20 iterations, RMS force 729.115<BR>step 214: EM did not converge in 20 iterations, RMS force 791.220<BR>step 215: EM did not converge in 20 iterations, RMS force 619.807<BR>step 216: EM did not converge in 20 iterations, RMS force 693.143<BR>step 217: EM did not converge in 20 iterations, RMS force 730.895<BR>step 218: EM did not converge in 20 iterations, RMS force 588.245<BR>step 219: EM did not converge in 20 iterations, RMS force 1110.880<BR>step 220: EM did not converge in 20
iterations, RMS force 1146.601<BR>step 221: EM did not converge in 20 iterations, RMS force 509.965<BR>step 222: EM did not converge in 20 iterations, RMS force 198.761<BR>step 223: EM did not converge in 20 iterations, RMS force 78.372<BR>step 224: EM did not converge in 20 iterations, RMS force 472.341<BR>step 225: EM did not converge in 20 iterations, RMS force 873.614<BR>step 226: EM did not converge in 20 iterations, RMS force 1676.297<BR>step 227: EM did not converge in 20 iterations, RMS force 1731.009</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 227: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates<BR>step 228: EM did not converge in 20 iterations, RMS force 0.040</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 228: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates<BR>step 229: EM did not converge in 20 iterations, RMS force 0.038<BR>step 230: EM did not converge in 20 iterations, RMS force 0.032</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 230: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates<BR>step 231: EM did not converge in 20 iterations, RMS force 0.033<BR>step 232: EM did not converge in 20 iterations, RMS force 0.032</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 232: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates<BR>step 233: EM did not converge in 20 iterations, RMS force 0.032<BR>step 234: EM did not converge in 20 iterations, RMS force 0.032<BR>step 235: EM did not converge in 20 iterations, RMS force 0.032<BR>step 236: EM did not converge in 20 iterations, RMS force 695.555<BR><BR>step 324: EM did not converge in 20 iterations, RMS force 2254.332<BR>step 325: EM did not converge in 20 iterations, RMS force 1366.153</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 325: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates<BR>step 326: EM did not converge in 20 iterations, RMS force 4453.299</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">step 326: Water molecule starting at atom 2641 can not be settled.<BR>Check for bad contacts and/or reduce the timestep if appropriate.<BR>Wrote pdb files with previous and current coordinates</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">-------------------------------------------------------<BR>Program mdrun, VERSION 4.5.4<BR>Source code file: pme.c, line: 538</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">Fatal error:<BR>2 particles communicated to PME node 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.<BR>This usually means that your system is not well equilibrated.<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors" target=_blank>http://www.gromacs.org/Documentation/Errors</A><BR></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">ion parameters:</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">; Topology file for Polarizable Alkali and Halide Ions in conjuction with SWM4-NDP water model<BR>; <BR>; Yu, H. B.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V. M.; MacKerell, A. D.; Roux, B.<BR>; Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field<BR>; J. Chem. Theory Comput. 2010, 6 (3), 774-786.</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>F 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Fc 1 F Fc 1 1.319199 <BR>2 Fs 1 F Fs 1 -2.319199 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.001786 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>CL 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 CLc 1 CL CLc 1 2.457187<BR>2 CLs 1 CL CLs 1 -3.457187</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.003969</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>BR 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 BRc 1 BR BRc 1 2.980713 <BR>2 BRs 1 BR BRs 1 -3.980713 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.005262 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>I 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Ic 1 I Ic 1 3.733085 <BR>2 Is 1 I Is 1 -4.733085 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.007439 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>LI 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 LIc 1 LI LIc 1 1.310427 <BR>2 LIs 1 LI LIs 1 -0.310427 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.000032 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>NA 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 NAc 1 NA NAc 1 1.687597 <BR>2 NAs 1 NA NAs 1 -0.687597 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.000157 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>K 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Kc 1 K Kc 1 2.580968 <BR>2 Ks 1 K Ks 1 -1.580968 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00083</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>RB 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 RBc 1 RB RBc 1 3.031161 <BR>2 RBs 1 RB RBs 1 -2.031161 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00137 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>CS 1</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 CSc 1 CS CSc 1 3.665877 <BR>2 CSs 1 CS CSs 1 -2.665877 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00236</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1<BR></SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">SWM4-NDP water model:</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">; <BR>; Topology file for SSWM4-NDP<BR>;<BR>; Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D.<BR>; A polarizable model of water for molecular dynamics simulations of biomolecules. <BR>; Chem. Phys. Lett. 2006, 418 (1-3), 245-249.<BR>;<BR>; Possible defines that you can put in your topol.top:<BR>; -FLEXIBLE Flexible model <BR>; -DPOSRES_WATER Position restrain oxygen atoms<BR>;</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ moleculetype ]<BR>; molname nrexcl<BR>SOL 2</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ atoms ]<BR>; id at type res nr res name at name cg nr charge mass<BR> 1 OW_swm4ndp 1 SOL OW 1 1.71636 15.99940<BR> 2 HW_swm4ndp 1 SOL HW1 1 0.55733 1.00800<BR> 3 HW_swm4ndp 1 SOL HW2 1 0.55733 1.00800<BR> 4 MW_swm4ndp 1
SOL MW 1 -1.11466 0.00000<BR> 5 OD_swm4ndp 1 SOL OD 1 -1.71636 0.00000</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 5 1 0.00097825 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">#ifndef FLEXIBLE</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ settles ]<BR>; i funct doh dhh<BR>1 1 0.09572 0.15139</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">#else</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ bonds ]<BR>; i j funct length force.c.<BR>1 2 1 0.09572 502416.0 <BR>1 3 1 0.09572 502416.0 <BR> <BR>[ angles ]<BR>; i j k funct angle force.c.<BR>2 1 3 1 104.52 628.02 </SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">#endif</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px"><BR>[ dummies3 ]<BR>; The position of the dummies is computed as follows:<BR>;<BR>; O<BR>; <BR>; D<BR>; <BR>; H H<BR>;<BR>; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]<BR>; 0.024034 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]<BR>; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)<BR>;<BR>; Dummy from funct a b<BR>4 1 2 3 1 0.205109464 0.205109464</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px">[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2 3 4 5<BR>2 1 3 4 5<BR>3 1 2 4 5<BR>4 1 2 3 5<BR>5 1 2 3 4</SPAN></DIV>
<DIV><SPAN style="FONT-SIZE: 16px"> </DIV></SPAN></td></tr></table>