Dear experts,<br><br>For hexane molecule I used atom types<br><br>opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols<br>opls_158 12.01100 ; all-atom C: CH, alcohols <br><br>in residue file:<br><br>[ HEX ]<br> [ atoms ]<br>
C1 opls_157 -0.180 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> H13 opls_140 0.060 1<br> C2 opls_158 -0.120 2<br> H21 opls_140 0.060 2<br>
H22 opls_140 0.060 2<br> C3 opls_158 -0.120 3<br> H31 opls_140 0.060 3<br> H32 opls_140 0.060 3<br> C4 opls_158 -0.120 4<br> H41 opls_140 0.060 4<br>
H42 opls_140 0.060 4<br> C5 opls_158 -0.120 5<br> H51 opls_140 0.060 5<br> H52 opls_140 0.060 5<br> C6 opls_157 -0.180 6<br> H61 opls_140 0.060 6<br>
H62 opls_140 0.060 6<br> H63 opls_140 0.060 6<br><br>now that I am trying to create top file for polyethylene (PE) I doubt if I pickec right atom types for hexane since I see in ffoplsaa.atp file:<br>
<br>opls_135 12.01100 ; alkane CH3<br> opls_136 12.01100 ; alkane CH2<br><br>for alkanes. Please let me know if I am right and I should use <br><br>opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols<br>opls_158 12.01100 ; all-atom C: CH, alcohols<br>
<br>for PE. or maybe this dies not affect the results since charges and mass are the same..?! <br><br>Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the suitable atom type for carbon atoms on PE chain?<br>
<br>2- I spent alot of time finding a solution for the following problem: I am trying to build up a very long PE chain. to do this I am using the following residues in rtp file:<br><br>; Polyethylene - this is an internal residue<br>
[ Eth ]<br> [ atoms ]<br> C1 opls_136 -0.120 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> C2 opls_136 -0.120 2<br> H21 opls_140 0.060 2<br> H22 opls_140 0.060 2<br>
[ bonds ]<br> C1 -C2<br> C1 H11<br> C1 H12<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 +C1<br><br>; Terminal PE residue ("beginning" of chain)<br>; designation arbitrary, C1 is -CH3<br>
; designation arbitrary, C1 is -CH3<br>[ EthB ]<br> [ atoms ]<br> C1 opls_135 -0.180 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> H13 opls_140 0.060 1<br> C2 opls_136 -0.120 2<br>
H21 opls_140 0.060 2<br> H22 opls_140 0.060 2<br> [ bonds ]<br> C1 H11<br> C1 H12<br> C1 H13<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 +C<br><br>; Terminal PE residue ("end" of chain)<br>
; designation arbitrary, C2 is -CH3<br>[ EthE ]<br> [ atoms ]<br> C1 opls_136 -0.120 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> C2 opls_135 -0.180 2<br> H21 opls_140 0.060 2<br>
H22 opls_140 0.060 2<br> H23 opls_140 0.060 2<br> [ bonds ]<br> C1 -C<br> C1 H11<br> C1 H12<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 H23<br><br>However, the software I am using(Ascalaph Desingner) to build up PE chain lists atoms as shown below: (I changed the res names to Eth and EthB myself). i.e. atoms have no numbering meaning that if I want to use the above resudies in rtp file I will have to go thorough the whole structure file(below) and do the numbering by myself (H to H11, H12, H21, H22...)and C to C1 C2) which is a tedious work. when I want to generate a molecule of 40000 Mw (about 1400 monomer units! or about 8000 atoms) <br>
<br>HETATM 1 CB EthB 1 2.739 2.554 -0.012 0.00 -0.39 C <br>HETATM 2 H EthB 1 2.736 3.644 -0.012 0.00 0.13 H <br>HETATM 3 H EthB 1 2.190 2.217 -0.893 0.00 0.13 H <br>
HETATM 4 H EthB 1 2.190 2.217 0.868 0.00 0.13 H <br>HETATM 5 C Eth 2 4.155 1.993 -0.012 0.00 -0.26 C <br>HETATM 6 H Eth 2 4.696 2.362 -0.887 0.00 0.13 H <br>
HETATM 7 H Eth 2 4.696 2.362 0.862 0.00 0.13 H <br>HETATM 8 C Eth 3 4.163 0.470 -0.012 0.00 -0.26 C <br>HETATM 9 H Eth 3 3.623 0.101 0.862 0.00 0.13 H <br>
HETATM 10 H Eth 3 3.623 0.101 -0.887 0.00 0.13 H <br>HETATM 11 C Eth 4 5.579 -0.091 -0.012 0.00 -0.26 C <br>HETATM 12 H Eth 4 6.119 0.278 -0.887 0.00 0.13 H <br>
.<br>.<br>I numbered 350 atoms (60 monomer units) and simulation is working now. <br>56<br> 1EthB C1 1 0.860 2.362 1.500<br> 1EthB H11 2 0.860 2.471 1.500<br> 1EthB H12 3 0.805 2.329 1.412<br>
1EthB H13 4 0.805 2.329 1.588<br> 1EthB C2 5 1.002 2.306 1.500<br> 1EthB H21 6 1.056 2.343 1.412<br> 1EthB H22 7 1.056 2.343 1.587<br> 2Eth C1 8 1.002 2.154 1.500<br>
2Eth H11 9 0.948 2.117 1.587<br> 2Eth H12 10 0.948 2.117 1.412<br> 2Eth C2 11 1.144 2.098 1.500<br> 2Eth H21 12 1.198 2.135 1.412<br> 2Eth H22 13 1.198 2.135 1.587<br>
3Eth C1 14 1.145 1.946 1.500<br> 3Eth H11 15 1.091 1.909 1.587<br> 3Eth H12 16 1.091 1.909 1.412<br> 3Eth C2 17 1.286 1.890 1.500<br> 3Eth H21 18 1.340 1.926 1.412<br>
3Eth H22 19 1.340 1.926 1.587<br> 4Eth C1 20 1.287 1.737 1.500<br> 4Eth H11 21 1.233 1.700 1.587<br> 4Eth H12 22 1.233 1.700 1.412<br> 4Eth C2 23 1.429 1.681 1.500<br>
4Eth H21 24 1.483 1.718 1.412<br> 4Eth H22 25 1.483 1.718 1.587<br> 5Eth C1 26 1.429 1.529 1.500<br><br>Nevertheless, I am trying to find out a better way to perform simulation for very longer chain. I examined x2top command to het top file with no atoms numbers (structure file .pdb above) and got gro file using editconf :<br>
<br>56<br> 1EthB CB 1 0.860 2.362 1.500<br> 1EthB H 2 0.859 2.471 1.500<br> 1EthB H 3 0.805 2.328 1.412<br> 1EthB H 4 0.805 2.328 1.588<br> 2Eth C 5 1.001 2.306 1.500<br>
2Eth H 6 1.055 2.343 1.413<br> 2Eth H 7 1.055 2.343 1.587<br> 3Eth C 8 1.002 2.153 1.500<br> 3Eth H 9 0.948 2.116 1.587<br> 3Eth H 10 0.948 2.116 1.413<br>
4Eth C 11 1.144 2.097 1.500<br> 4Eth H 12 1.198 2.134 1.413<br> 4Eth H 13 1.198 2.134 1.587<br> 5Eth C 14 1.145 1.945 1.500<br> 5Eth H 15 1.090 1.908 1.587<br>
5Eth H 16 1.090 1.908 1.413<br> 6Eth C 17 1.286 1.889 1.500<br> 6Eth H 18 1.340 1.926 1.413<br> 6Eth H 19 1.340 1.926 1.587<br> 7Eth C 20 1.287 1.736 1.500<br>
7Eth H 21 1.233 1.700 1.587<br><br><br>The top file I got has contains exactly the same listing of [bonds] [pairs] [angles] [dihedrals] as the one I got from the structure file for which I did the numbering by hand. But I am unsure of the forcefield parameters if they are extracted from itp file properly because after doing energy minimization step I get LINCS error.<br>
<br>Back Off! I just backed up ener.edr to ./#ener.edr.1#<br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 200<br>Step= 0, Dmax= 1.0e-02 nm, Epot= 5.25663e+04 Fmax= 2.91635e+03, atom= 53<br>
Step= 1, Dmax= 1.0e-02 nm, Epot= 5.20487e+04 Fmax= 6.27470e+03, atom= 1<br>Step= 2, Dmax= 1.2e-02 nm, Epot= 5.12076e+04 Fmax= 5.74320e+03, atom= 56<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 5.08573e+04 Fmax= 4.77251e+03, atom= 7<br>
Step= 4, Dmax= 1.7e-02 nm, Epot= 5.04166e+04 Fmax= 7.91400e+03, atom= 53<br>Step= 5, Dmax= 2.1e-02 nm, Epot= 4.88521e+04 Fmax= 1.11208e+04, atom= 7<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 4.66591e+04 Fmax= 8.34560e+03, atom= 48<br>
<br>Step 7, time 0.014 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.005015, max 0.011148 (between atoms 5 and 6)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
Step= 7, Dmax= 3.0e-02 nm, Epot= 4.41164e+04 Fmax= 1.36155e+04, atom= 23<br>Step= 8, Dmax= 3.6e-02 nm, Epot= 4.22917e+04 Fmax= 8.05183e+03, atom= 23<br><br>Step 9, time 0.018 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.022162, max 0.109777 (between atoms 23 and 25)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 23 25 51.2 0.1086 0.1210 0.1090<br> 23 24 44.4 0.1090 0.1150 0.1090<br>
8 10 32.1 0.1100 0.1113 0.1090<br>Step= 10, Dmax= 2.1e-02 nm, Epot= 4.13912e+04 Fmax= 1.80418e+04, atom= 23<br>Step= 11, Dmax= 2.6e-02 nm, Epot= 4.03985e+04 Fmax= 6.68523e+03, atom= 39<br>Step= 12, Dmax= 3.1e-02 nm, Epot= 3.98609e+04 Fmax= 3.40293e+04, atom= 23<br>
Step= 13, Dmax= 3.7e-02 nm, Epot= 3.88153e+04 Fmax= 6.68366e+03, atom= 23<br><br><br>.<br>.<br>.<br><br>Q 2-1 Please kindly furnish me with your comments on this issue. <b>I need a residue for internal ethylene monomer in rtp file which depends as less as possible on atoms numbering (H11,...). </b>I think the solution will help many gmx users dealing with polymers. what would be the best approach?<br>
<br>my current internal repeating unit has numbering of atoms:<br>[Eth ]<br>
[ atoms ]<br>
C1 opls_136 -0.120 1<br>
H11 opls_140 0.060 1<br>
H12 opls_140 0.060 1<br>
C2 opls_136 -0.120 2<br>
H21 opls_140 0.060 2<br>
H22 opls_140 0.060 2<br>
[ bonds ]<br>
C1 -C2<br>
C1 H11<br>
C1 H12<br>
C1 C2<br>
C2 H21<br>
C2 H22<br>
C2 +C1<br><br>Q 2-2. Does x2top command have advantage over pdb2gmx command with regards to atom numbering? <br><br>Many many thanks,<br>Best,<br>Moeed<br><input type="hidden"><input type="hidden"><div></div>