<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><FONT style="BACKGROUND-COLOR: #cce8cf">Dear GMX users,</FONT></DIV>
<DIV><FONT style="BACKGROUND-COLOR: #cce8cf"> I am using GMX4.5.4 to simulate SWM4-NDP polarizable water model, it is OK. But when I use the ions polarizable model which is in conjuction with SWM4-NDP model, the <STRONG>RMS force is very large:</STRONG></FONT></DIV>
<DIV>step 16: EM did not converge in 20 iterations, RMS force 7.950<BR>step 17: EM did not converge in 20 iterations, RMS force 61.192<BR>step 18: EM did not converge in 20 iterations, RMS force 177.091<BR>step 19: EM did not converge in 20 iterations, RMS force 371.756<BR>step 20: EM did not converge in 20 iterations, RMS force 624.178<BR>step 21: EM did not converge in 20 iterations, RMS force 849.728<BR>step 22: EM did not converge in 20 iterations, RMS force 891.695<BR>step 23: EM did not converge in 20 iterations, RMS force 830.527<BR>step 24: EM did not converge in 20 iterations, RMS force 803.412<BR>step 25: EM did not converge in 20 iterations, RMS force 882.106<BR>step 26: EM did not converge in 20 iterations, RMS force 1031.051<BR>step 27: EM did not converge in 20 iterations, RMS force 1339.648<BR>step 28: EM did not converge in 20 iterations, RMS force 1727.688<BR>step 29: EM did not converge in 20 iterations, RMS force 1750.876<BR>step 30:
EM did not converge in 20 iterations, RMS force 1445.519<BR>step 31: EM did not converge in 20 iterations, RMS force 0.033<BR>step 32: EM did not converge in 20 iterations, RMS force 1210.740<BR>step 33: EM did not converge in 20 iterations, RMS force 526.515<BR>step 34: EM did not converge in 20 iterations, RMS force 0.033<BR>step 35: EM did not converge in 20 iterations, RMS force 0.032<BR>step 36: EM did not converge in 20 iterations, RMS force 0.032<BR>step 37: EM did not converge in 20 iterations, RMS force 0.033<BR>step 38: EM did not converge in 20 iterations, RMS force 0.032<BR>step 39: EM did not converge in 20 iterations, RMS force 0.031<BR>step 40: EM did not converge in 20 iterations, RMS force 0.032<BR>step 41: EM did not converge in 20 iterations, RMS force 0.032<BR>step 42: EM did not converge in 20 iterations, RMS force 0.032<BR>step 43: EM did not converge in 20 iterations, RMS force 0.032<BR>step 44: EM did not converge in 20
iterations, RMS force 0.032<BR>step 45: EM did not converge in 20 iterations, RMS force 0.032<BR>step 46: EM did not converge in 20 iterations, RMS force 0.033<BR>step 47: EM did not converge in 20 iterations, RMS force 0.032<BR>step 48: EM did not converge in 20 iterations, RMS force 0.033<BR>step 49: EM did not converge in 20 iterations, RMS force 0.032<BR>step 50: EM did not converge in 20 iterations, RMS force 0.032<BR>step 51: EM did not converge in 20 iterations, RMS force 0.033<BR>step 52: EM did not converge in 20 iterations, RMS force 0.032<BR>step 53: EM did not converge in 20 iterations, RMS force 0.033<BR>step 54: EM did not converge in 20 iterations, RMS force 0.032<BR>step 55: EM did not converge in 20 iterations, RMS force 0.032<BR>step 56: EM did not converge in 20 iterations, RMS force 0.032<BR>step 57: EM did not converge in 20 iterations, RMS force 0.032<BR>step 58: EM did not converge in 20 iterations, RMS force 0.032<BR>step 59: EM
did not converge in 20 iterations, RMS force 0.032<BR>step 60: EM did not converge in 20 iterations, RMS force 0.032<BR>step 61: EM did not converge in 20 iterations, RMS force 0.032<BR>step 62: EM did not converge in 20 iterations, RMS force 0.032<BR>step 63: EM did not converge in 20 iterations, RMS force 2.835<BR>step 64: EM did not converge in 20 iterations, RMS force 120.556<BR>step 65: EM did not converge in 20 iterations, RMS force 346.147<BR>step 66: EM did not converge in 20 iterations, RMS force 634.393<BR>step 67: EM did not converge in 20 iterations, RMS force 904.684<BR>step 68: EM did not converge in 20 iterations, RMS force 1133.427<BR>step 69: EM did not converge in 20 iterations, RMS force 735.408<BR>step 70: EM did not converge in 20 iterations, RMS force 948.153<BR>step 71: EM did not converge in 20 iterations, RMS force 967.569<BR>step 72: EM did not converge in 20 iterations, RMS force 630.741<BR>step 73: EM did not converge in 20
iterations, RMS force 1035.501<BR>step 74: EM did not converge in 20 iterations, RMS force 698.937<BR>step 75: EM did not converge in 20 iterations, RMS force 1179.575<BR>step 76: EM did not converge in 20 iterations, RMS force 765.233<BR>step 77: EM did not converge in 20 iterations, RMS force 939.995<BR>step 78: EM did not converge in 20 iterations, RMS force 131.329<BR>step 79: EM did not converge in 20 iterations, RMS force 51.797<BR>step 80: EM did not converge in 20 iterations, RMS force 405.775<BR>step 81: EM did not converge in 20 iterations, RMS force 161.922<BR>step 82: EM did not converge in 20 iterations, RMS force 565.036<BR>step 83: EM did not converge in 20 iterations, RMS force 1014.157<BR>step 84: EM did not converge in 20 iterations, RMS force 1136.628<BR>step 85: EM did not converge in 20 iterations, RMS force 0.033<BR>step 86: EM did not converge in 20 iterations, RMS force 307.819<BR>step 87: EM did not converge in 20 iterations,
RMS force 0.032<BR>step 88: EM did not converge in 20 iterations, RMS force 52.057<BR>step 89: EM did not converge in 20 iterations, RMS force 0.032<BR>step 90: EM did not converge in 20 iterations, RMS force 0.032<BR>step 91: EM did not converge in 20 iterations, RMS force 0.033<BR>step 92: EM did not converge in 20 iterations, RMS force 251.725<BR>step 93: EM did not converge in 20 iterations, RMS force 0.032<BR>step 94: EM did not converge in 20 iterations, RMS force 0.033<BR>step 95: EM did not converge in 20 iterations, RMS force 0.033<BR>step 96: EM did not converge in 20 iterations, RMS force 0.033<BR>step 97: EM did not converge in 20 iterations, RMS force 0.032<BR>step 98: EM did not converge in 20 iterations, RMS force 0.032<BR>step 99: EM did not converge in 20 iterations, RMS force 0.032<BR>step 100: EM did not converge in 20 iterations, RMS force 0.032<BR>step 101: EM did not converge in 20 iterations, RMS force 0.032<BR>step 102: EM did
not converge in 20 iterations, RMS force 0.032<BR>step 103: EM did not converge in 20 iterations, RMS force 0.032<BR>step 104: EM did not converge in 20 iterations, RMS force 0.034<BR>step 105: EM did not converge in 20 iterations, RMS force 0.033<BR>step 106: EM did not converge in 20 iterations, RMS force 0.033<BR>step 107: EM did not converge in 20 iterations, RMS force 0.032<BR>step 108: EM did not converge in 20 iterations, RMS force 0.032<BR>step 109: EM did not converge in 20 iterations, RMS force 0.032<BR>step 110: EM did not converge in 20 iterations, RMS force 0.032<BR>step 111: EM did not converge in 20 iterations, RMS force 0.032<BR>step 112: EM did not converge in 20 iterations, RMS force 0.032<BR>step 113: EM did not converge in 20 iterations, RMS force 0.032<BR>step 114: EM did not converge in 20 iterations, RMS force 0.032<BR>step 115: EM did not converge in 20 iterations, RMS force 0.032<BR>step 116: EM did not converge in 20
iterations, RMS force 0.032<BR>step 117: EM did not converge in 20 iterations, RMS force 0.032<BR>step 118: EM did not converge in 20 iterations, RMS force 0.032<BR>step 119: EM did not converge in 20 iterations, RMS force 0.032<BR>step 120: EM did not converge in 20 iterations, RMS force 0.032<BR>step 121: EM did not converge in 20 iterations, RMS force 0.032<BR>step 122: EM did not converge in 20 iterations, RMS force 0.033<BR>step 123: EM did not converge in 20 iterations, RMS force 0.033<BR>step 124: EM did not converge in 20 iterations, RMS force 0.031<BR>step 125: EM did not converge in 20 iterations, RMS force 0.032<BR>step 126: EM did not converge in 20 iterations, RMS force 0.033<BR>step 127: EM did not converge in 20 iterations, RMS force 0.031<BR>step 128: EM did not converge in 20 iterations, RMS force 0.033<BR>step 129: EM did not converge in 20 iterations, RMS force 0.031<BR>step 130: EM did not converge in 20 iterations, RMS force
0.032<BR>step 131: EM did not converge in 20 iterations, RMS force 0.033<BR>step 132: EM did not converge in 20 iterations, RMS force 0.032<BR>step 133: EM did not converge in 20 iterations, RMS force 0.032<BR>......</DIV>
<DIV> </DIV>
<DIV>the swm4-ndp model :</DIV>
<DIV>; <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>;</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>SOL 2</DIV>
<DIV>[ 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</DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 5 1 0.00097825 </DIV>
<DIV>#ifndef FLEXIBLE</DIV>
<DIV>[ settles ]<BR>; i funct doh dhh<BR>1 1 0.09572 0.15139</DIV>
<DIV>#else</DIV>
<DIV>[ 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 </DIV>
<DIV>#endif</DIV>
<DIV><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</DIV>
<DIV>[ 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</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>the ion parameters in conjuction with it:</DIV>
<DIV>; 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.</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>F 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Fc 1 Fc Fc 1 1.319199 <BR>2 Fs 1 Fs Fs 1 -2.319199 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.001786 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>CL 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 CLc 1 CLc CLc 1 2.457187<BR>2 CLs 1 CLs CLs 1 -3.457187</DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.003969</DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>BR 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 BRc 1 BRc BRc 1 2.980713 <BR>2 BRs 1 BRs BRs 1 -3.980713 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.005262 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>I 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Ic 1 Ic Ic 1 3.733085 <BR>2 Is 1 Is Is 1 -4.733085 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.007439 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>LI 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 LIc 1 LIc LIc 1 1.310427 <BR>2 LIs 1 LIs LIs 1 -0.310427 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.000032 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>NA 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 NAc 1 NAc NAc 1 1.687597 <BR>2 NAs 1 NAs NAs 1 -0.687597 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.000157 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>K 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 Kc 1 Kc Kc 1 2.580968 <BR>2 Ks 1 Ks Ks 1 -1.580968 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00083</DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>RB 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 RBc 1 RBc RBc 1 3.031161 <BR>2 RBs 1 RBs RBs 1 -2.031161 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00137 </DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>CS 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge<BR>1 CSc 1 CSc CSc 1 3.665877 <BR>2 CSs 1 CSs CSs 1 -2.665877 </DIV>
<DIV>[ polarization ]<BR>; See notes above. alpha (nm^3)<BR>1 2 1 0.00236</DIV>
<DIV>[ exclusions ]<BR>; iatom excluded from interaction with i<BR>1 2<BR>2 1<BR></DIV>
<DIV> </DIV>
<DIV>Anybody could give me some helps ?</DIV>
<DIV>Thanks in advance!</DIV>
<DIV> </DIV>
<DIV>ZHONGJIN HE</DIV></td></tr></table>