Dear experts,<br><br>I am trying to exclude all nonbonded interaction on hexane molecule. <br><br><br>1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc<br><br>mdrun -rerun -<b>x breakdown.xtc</b> -s Hexane-Stack125_md.tpr <b>-o ORIGINAL-Trajectory-NOexcl.tpr</b> -c Hexane-Stack125_after_md -v >&
output.mdrun_m<br><br>2-Can you please check exclsusions directive in top file. I have used also nrexcl 5 in molecule top. does this make sense given that I have defined all the possible exclusions in 19 lines.<br><br><br>
<br><br>********************grompp em :<br><br>*checking input for internal consistency...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>
Excluding 5 bonded neighbours molecule type 'Hexane'<br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>
processing index file...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>Making dummy/rest group for T-Coupling containing 2500 elements<br>Making dummy/rest group for Acceleration containing 2500 elements<br>
Making dummy/rest group for Freeze containing 2500 elements<br>Making dummy/rest group for Energy Mon. containing 2500 elements<br>Making dummy/rest group for VCM containing 2500 elements<br>Number of degrees of freedom in T-Coupling group rest is 5122.00<br>
Making dummy/rest group for User1 containing 2500 elements<br>Making dummy/rest group for User2 containing 2500 elements<br>Making dummy/rest group for XTC containing 2500 elements<br>Making dummy/rest group for Or. Res. Fit containing 2500 elements<br>
Making dummy/rest group for QMMM containing 2500 elements<br>T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>
User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>
Checking consistency between energy and charge groups...<br><br>NOTE 1 [file em.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br> You might want to consider using PME electrostatics.<br>
<br><br>writing run input file...<br><br>There was 1 note<br><br>Back Off! I just backed up Hexane-Stack125_em.tpr to ./#Hexane-Stack125_em.tpr.4#<br><br>gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family?" (Gogol Bordello)<br>
<br> :-) G R O M A C S (-:<br><br> Getting the Right Output Means no Artefacts in Calculating Stuff<br><br> :-) VERSION 4.0.7 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br>
Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br>
<br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br>
of the License, or (at your option) any later version.<br><br> :-) grompp (double precision) (-:<br><br>processing topology...<br>turning all bonds into constraints...<br>Analysing residue names:<br>
There are: 125 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>This run will generate roughly 1 Mb of data<br><br>********************************************************************output md_em:<br>
<br><br>teepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 200<br>Step= 0, Dmax= 1.0e-02 nm, Epot= -2.41657e+03 Fmax= 1.96636e+02, atom= 1189<br><br>writing lowest energy coordinates.<br>
<br>Back Off! I just backed up Hexane-Stack125_b4pr.gro to ./#Hexane-Stack125_b4pr.gro.4#<br><br>Steepest Descents converged to Fmax < 1000 in 1 steps<br>Potential Energy = -2.41656779590808e+03<br>Maximum force = 1.96635853696765e+02 on atom 1189<br>
Norm of force = 1.37247833599652e+02<br>******************************************************************************************************out put grompp md<br><br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 5 bonded neighbours molecule type 'Hexane'<br>processing coordinates...<br>double-checking input for internal consistency...<br>
Velocities were taken from a Maxwell distribution at 300 K<br>renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>
Making dummy/rest group for Acceleration containing 2500 elements<br>Making dummy/rest group for Freeze containing 2500 elements<br>Making dummy/rest group for Energy Mon. containing 2500 elements<br>Making dummy/rest group for VCM containing 2500 elements<br>
Number of degrees of freedom in T-Coupling group HEX is 5122.00<br>Making dummy/rest group for User1 containing 2500 elements<br>Making dummy/rest group for User2 containing 2500 elements<br>Making dummy/rest group for XTC containing 2500 elements<br>
Making dummy/rest group for Or. Res. Fit containing 2500 elements<br>Making dummy/rest group for QMMM containing 2500 elements<br>T-Coupling has 1 element(s): HEX<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>Estimate for the relative computational load of the PME mesh part: 0.13<br>writing run input file...<br><br>There was 1 note<br>
<br>Back Off! I just backed up Hexane-Stack125_md.tpr to ./#Hexane-Stack125_md.tpr.1#<br><br>gcq#190: "Load Up Your Rubber Bullets" (10 CC)<br><br> :-) G R O M A C S (-:<br><br> Gravel Rubs Often Many Awfully Cauterized Sores<br>
<br> :-) VERSION 4.0.7 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
Copyright (c) 2001-2008, The GROMACS development team,<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br>
modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br>
:-) grompp (double precision) (-:<br><br>processing topology...<br>turning all bonds into constraints...<br>Analysing residue names:<br>There are: 125 OTHER residues<br>There are: 0 PROTEIN residues<br>
There are: 0 DNA residues<br>Analysing Other...<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 42x21x21, spacing 0.119 0.119 0.119<br>This run will generate roughly 65 Mb of data<br>
***********************************************************************<br><br><br><br><br><br><br><br><br><br><br><br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br>
<br>[ moleculetype ]<br>; Name nrexcl<br>Hexane 5<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot -0.18<br>
2 opls_140 1 HEX H11 1 0.06 1.008 ; qtot -0.12<br> 3 opls_140 1 HEX H12 1 0.06 1.008 ; qtot -0.06<br> 4 opls_140 1 HEX H13 1 0.06 1.008 ; qtot 0<br>
5 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot -0.12<br> 6 opls_140 1 HEX H21 2 0.06 1.008 ; qtot -0.06<br> 7 opls_140 1 HEX H22 2 0.06 1.008 ; qtot 0<br>
8 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot -0.12<br> 9 opls_140 1 HEX H31 3 0.06 1.008 ; qtot -0.06<br> 10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot 0<br>
11 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot -0.12<br> 12 opls_140 1 HEX H41 4 0.06 1.008 ; qtot -0.06<br> 13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot 0<br>
14 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot -0.12<br> 15 opls_140 1 HEX H51 5 0.06 1.008 ; qtot -0.06<br> 16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot 0<br>
17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot -0.18<br> 18 opls_140 1 HEX H61 6 0.06 1.008 ; qtot -0.12<br> 19 opls_140 1 HEX H62 6 0.06 1.008 ; qtot -0.06<br>
20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot 0<br><br>[ exclusions ]<br>1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>6 7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>7 8 9 10 11 12 13 14 15 16 17 18 19 20<br>8 9 10 11 12 13 14 15 16 17 18 19 20<br>
9 10 11 12 13 14 15 16 17 18 19 20<br>
10 11 12 13 14 15 16 17 18 19 20<br>11 12 13 14 15 16 17 18 19 20<br>12 13 14 15 16 17 18 19 20<br>13 14 15 16 17 18 19 20<br>14 15 16 17 18 19 20<br>15 16 17 18 19 20<br>16 17 18 19 20<br>17 18 19 20<br>18 19 20<br>19 20<br>
<br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br> 1 2 1 <br> 1 3 1 <br> 1 4 1 <br> 1 5 1 <br> 5 6 1 <br> 5 7 1 <br>
5 8 1 <br> 8 9 1 <br> 8 10 1 <br> 8 11 1 <br> 11 12 1 <br> 11 13 1 <br> 11 14 1 <br> 14 15 1 <br> 14 16 1 <br> 14 17 1 <br>
17 18 1 <br>
17 19 1 <br> 17 20 1 <br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br> 1 9 1 <br> 1 10 1 <br> 1 11 1 <br> 2 6 1 <br>
2 7 1 <br> 2 8 1 <br> 3 6 1 <br> 3 7 1 <br> 3 8 1 <br> 4 6 1 <br> 4 7 1 <br> 4 8 1 <br> 5 12 1 <br> 5 13 1 <br>
5 14 1 <br>
6 9 1 <br> 6 10 1 <br> 6 11 1 <br> 7 9 1 <br> 7 10 1 <br> 7 11 1 <br> 8 15 1 <br> 8 16 1 <br> 8 17 1 <br> 9 12 1 <br>
9 13 1 <br>
9 14 1 <br> 10 12 1 <br> 10 13 1 <br> 10 14 1 <br> 11 18 1 <br> 11 19 1 <br> 11 20 1 <br> 12 15 1 <br> 12 16 1 <br> 12 17 1 <br>
13 15 1 <br>
13 16 1 <br> 13 17 1 <br> 15 18 1 <br> 15 19 1 <br> 15 20 1 <br> 16 18 1 <br> 16 19 1 <br> 16 20 1 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br>
2 1 3 1 <br> 2 1 4 1 <br> 2 1 5 1 <br> 3 1 4 1 <br> 3 1 5 1 <br> 4 1 5 1 <br> 1 5 6 1 <br> 1 5 7 1 <br>
1 5 8 1 <br> 6 5 7 1 <br> 6 5 8 1 <br> 7 5 8 1 <br> 5 8 9 1 <br> 5 8 10 1 <br> 5 8 11 1 <br> 9 8 10 1 <br>
9 8 11 1 <br> 10 8 11 1 <br> 8 11 12 1 <br> 8 11 13 1 <br> 8 11 14 1 <br> 12 11 13 1 <br> 12 11 14 1 <br> 13 11 14 1 <br>
11 14 15 1 <br> 11 14 16 1 <br> 11 14 17 1 <br> 15 14 16 1 <br> 15 14 17 1 <br> 16 14 17 1 <br> 14 17 18 1 <br> 14 17 19 1 <br>
14 17 20 1 <br> 18 17 19 1 <br> 18 17 20 1 <br> 19 17 20 1 <br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br>
2 1 5 6 3 <br> 2 1 5 7 3 <br> 2 1 5 8 3 <br> 3 1 5 6 3 <br> 3 1 5 7 3 <br> 3 1 5 8 3 <br> 4 1 5 6 3 <br>
4 1 5 7 3 <br> 4 1 5 8 3 <br> 1 5 8 9 3 <br> 1 5 8 10 3 <br> 1 5 8 11 3 <br> 6 5 8 9 3 <br> 6 5 8 10 3 <br>
6 5 8 11 3 <br> 7 5 8 9 3 <br> 7 5 8 10 3 <br> 7 5 8 11 3 <br> 5 8 11 12 3 <br> 5 8 11 13 3 <br> 5 8 11 14 3 <br>
9 8 11 12 3 <br> 9 8 11 13 3 <br> 9 8 11 14 3 <br> 10 8 11 12 3 <br> 10 8 11 13 3 <br> 10 8 11 14 3 <br> 8 11 14 15 3 <br>
8 11 14 16 3 <br> 8 11 14 17 3 <br> 12 11 14 15 3 <br> 12 11 14 16 3 <br> 12 11 14 17 3 <br> 13 11 14 15 3 <br> 13 11 14 16 3 <br>
13 11 14 17 3 <br> 11 14 17 18 3 <br> 11 14 17 19 3 <br> 11 14 17 20 3 <br> 15 14 17 18 3 <br> 15 14 17 19 3 <br> 15 14 17 20 3 <br>
16 14 17 18 3 <br> 16 14 17 19 3 <br> 16 14 17 20 3 <br><br>; Include Position restraint file<br>;#ifdef POSRES<br>;#include "posre.itp"<br>;#endif<br><br>; Include water topology<br>
;#include "spc.itp"<br><br>;#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>;[ position_restraints ]<br>; i funct fcx fcy fcz<br> ; 1 1 1000 1000 1000<br>
;#endif<br><br>; Include generic topology for ions<br>;#include "ions.itp"<br><br>[ system ]<br>; Name<br>Hexane<br><br>[ molecules ]<br>; Compound #mols<br>Hexane 125<br><br>