Hi , <br> I am also working on similar systems. Can you tell me where and what LJ parameters you specified for halides<br><br>Thanks in advance,<br>Abhijeet<br><br><div class="gmail_quote">On Fri, Aug 12, 2011 at 8:56 AM, zhongjin <span dir="ltr"><<a href="mailto:zhongjin1000@yahoo.com.cn">zhongjin1000@yahoo.com.cn</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font:inherit" valign="top"><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 <b>RMS force is very large:</b></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></tbody></table><br>--<br>
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<br> Research Assistant
<br> Molecular Thermodynamics and Statistical Mechanics Research Group
<br> University of Wisconsin-Madison
<br> <a href="http://www.engr.wisc.edu/groups/mtsm/index.shtml" target="_blank">http://www.engr.wisc.edu/groups/mtsm/index.shtml</a>
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<br></div><div> </div></div><br>