Hi all!. I was trying to simulate a complex cation in MeCN solution and I got 2 strange warnings to me:
processing topology... WARNING 1 [file "ff_emi.itp", line 7]: Overriding atomtype CT WARNING 2 [file "ff_emi.itp", line 11]: Overriding atomtype H1 But I did found that strange because, as you can see in the file attached, the entries CT and H1 are just called once. A second thing that called my attention is the following line that grompp gives me: "Generating 1-4 interactions: fudge = 0.5". It's not wrong, since I put this fudge for the VdW interactions, BUT I also placed a different fudge for the intramolecular coulombic interations (0.8333), using these lines in the ".top" file I created: [ defaults ] ; nbfunc com-rule gen-pairs fudgeLJ fudgeQ 1 2 yes 0.5000 0.8333 Shouldn't grompp output two fudge parameters instead of only one? Are those known issues? I just found those warnings in case of use of standard force fields, what is not the case. The fudge output I could not find any possible answer. Thanks a lot for everything in advance. Jones
; ; emi Force Field Topology File ; [ atomtypes ] ; name mass (a.m.u.) charge (e) ptype sigma (nm) epsilon (kJ/mol) CT 12.0112 0.000 A 0.3400 0.4577 NA 14.0067 0.000 A 0.3250 0.7113 CR 12.0112 0.000 A 0.3400 0.3598 CW 12.0112 0.000 A 0.3400 0.3598 H1 1.0080 0.000 A 0.2471 0.0657 HC 1.0080 0.000 A 0.2649 0.0657 H5 1.0080 0.000 A 0.2421 0.0628 H4 1.0080 0.000 A 0.2511 0.0628 [ bondtypes ] ; i j funct b0 (nm) kb (kJ/mol.nm^2) CT NA 1 0.1475 141000.81 CT CT 1 0.1526 129704.00 NA CR 1 0.1343 199576.80 NA CW 1 0.1381 178656.80 CW CW 1 0.1350 229701.61 H1 CT 1 0.1090 142256.00 HC CT 1 0.1090 142256.00 H5 CR 1 0.1080 153552.80 H4 CW 1 0.1080 153552.80 [ angletypes ] ; i j k funct th0 (degree) kb (kJ/mol.rad^2) H1 CT H1 1 109.50 146.44 H1 CT NA 1 109.50 209.20 H1 CT CT 1 109.50 209.20 CT CT NA 1 109.50 209.20 HC CT HC 1 109.50 146.44 HC CT CT 1 109.50 209.20 CT NA CR 1 128.80 292.88 CT NA CW 1 121.20 292.88 CR NA CW 1 120.00 292.88 H5 CR NA 1 120.00 146.44 NA CR NA 1 120.00 292.88 H4 CW NA 1 120.00 146.44 H4 CW CW 1 119.70 146.44 NA CW CW 1 121.20 292.88 [ dihedraltypes ] ; j k funct phi (degree) cp (kJ/mol.rad^2) mult(n) CT NA 1 0.00 0.0000 2.0 CT CT 1 0.00 0.6510 3.0 CW CW 1 180.00 27.8236 2.0
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