<div>Thank you, Justin !<br><br> I have add the output generated by grompp and mdrun at the end.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">
Cun Zhang wrote:<br>
> hi, Justin. Thank you for your patience !<br>
><br>
> I'm still in trouble with infinite CNT simulation.<br>
><br>
> I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A)<br>
> with 832 atoms and water. I'm using x2top to generate the CNT.itp with<br>
> share-bonds. The idea is that I generate a (16,0) CNT(CNT_B) with 960<br>
> atoms ( more 4 layer than CNT_A. Each layer has 32 atoms ).<br>
> When I use CNT.itp generated by CNT_A and x2top, it works. But when I<br>
> use the CNT.itp which has share-bonds information, it can't work.<br>
><br>
><br>
> The process I'm doing CNT simulation is as follows:<br>
> # the CNT_new.pdb is a (16,0) CNT with 960 atoms.<br>
> # I add the custom forcefield parameters to tmp.top, and change the<br>
> number of a charge group to 32, then rename it CNT.itp at the end.<br>
><br>
> x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name<br>
> CNT<br>
><br>
> bash sharebond_script # create share bonds<br>
><br>
<br></div>
The script below is renumbering and removing atoms. Why are you doing this? I<br>
thought the purpose of CNT_new was to generate a larger structure?<br></blockquote><div><br>I
hope generate sharing bonds between the atoms at the top edge and the
atoms at the bottom edge of CNT by x2top. But the parameter -pbc does
not work. So I add 4 layers at the top of CNT.pdb and rename it
CNT_new.pdb, that is, the front 832 rows of them are same. <br>
<br>The
atoms of No. 833-960 in CNT_new.pdb can be seen the bottom 4 layers of
atoms of No.1-128 of CNT.pdb translated up a box hight. So after
generating the topology file and renaming atoms of No. 833-960 to
No.1-128 in the topology file (use the command 'x2top -nopbc') the
topology file of CNT_new.pdb should be the same as the topology file
of CNT.pdb with sharing bonds (and angles, diherals) ( use the command
'x2top -pbc' ). <br>
</div><div><br>That's why I write that script. Hope you understand
what I mean. Of course, The other reason is that I'm not familar with
how to generate CNT's topology file, so I use x2top to do it. That's
easier relatively.<br>
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
> editconf -f CNT.pdb -o -box 3.8 3.8 5.614<br>
><br>
<br></div>
Now you are manipulating CNT.pdb - is this the correct next step? If this<br>
actually pertains to CNT_new.pdb, then the box size is insufficient to hold the<br>
larger structure. But now I'm just confused as to what you're doing.<br></blockquote><div><br>This is the information when I run this command. I think it's ok.<div class="im"><br><div style="margin-left: 40px;">
system size : 1.270 1.270 5.472 (nm)<br>
center : -0.000 0.000 2.736 (nm)<br>box vectors : 0.000 0.000 0.000 (nm)<br>box angles : 0.00 0.00 0.00 (degrees)<br>box volume : 0.00 (nm^3)<br>shift : 1.900 1.900 0.071 (nm)<br>
</div><div style="margin-left: 40px;">new center : 1.900 1.900 2.807 (nm)<br>new box vectors : 3.800 3.800 5.614 (nm)<br>new box angles : 90.00 90.00 90.00 (degrees)<br>new box volume : 81.07 (nm^3)<br>
</div><br></div></div><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
> genbox -cp out -cs -p CNT -o b4em.pdb #The simulation box size can be<div class="im"><br>
> seen in b4em.pdb<br>
><br>
> pymol b4em.pdb #remove water. After editing it,I save it as b4em.pdb<br>
> too.Now the information about box size is losing. I don't know why.I'm<br>
> not familar with it :)<br>
><br>
> editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information<br>
> about box size<br>
> vim CNT.top #change the number of water to make it the same as b4em.pdb<br>
> grompp -f em -o em -c b4em -p CNT -maxwarn 5<br>
> mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em<br>
<br></div>
Does energy minimization work? What did the potential energy and maximum force<br>
converge to? Again, what is the purpose of "-maxwarn 5"? Are there errors that<br>
grompp is generating that you are simply trying to bypass? This is generally a<br>
bad idea.<br></blockquote><div><br> Yes, EM work.<br><div style="margin-left: 40px;">Steepest Descents converged to Fmax < 1000 in 9 steps<br>Potential Energy = -9.5444641e+04<br>Maximum force = 8.6610358e+02 on atom 832<br>
Norm of force = 2.2713820e+02<br></div></div><br><div class="im">There are two notes,no warnings,no errors when grompp.<br>When I run the MD,errors come:<br><div style="margin-left: 40px;">500000 steps, 250.0 ps.<br>
There were 64 inconsistent shifts. Check your topology<br>
step 0<br>t = 0.003 ps: Water molecule starting at atom 7226 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br><br>t = 0.004 ps: Water molecule starting at atom 7217 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br><br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.5<br>Source code file: ../../../../src/mdlib/nsgrid.c, line: 357<br>
<br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>based on its coordinates. If your system contains collisions or parameter<br>errors that give particles very high velocities you might end up with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>
energy seems reasonable before trying again.<br><br>Variable ci has value -2147483648. It should have been within [ 0 .. 200 ]<br></div><br><br>The output of grompp and mdrun are there.<br><br><div style="margin-left: 40px;">
cunzhang@Debian:~/CNT$ grompp -f em -o em -c b4em -p CNT -maxwarn 5<br>==help information==<br>Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>checking input for internal consistency...<br>
processing topology...<br>Opening library file /usr/share/gromacs/top/ffgmx.itp<br>Opening library file /usr/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/share/gromacs/top/ff_dum.itp<br>
Generated 1337 of the 1540 non-bonded parameter combinations<br>Opening library file /usr/share/gromacs/top/spce.itp<br>Excluding 3 bonded neighbours molecule type 'CNT'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>
processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br><br><br>NOTE 1 [file CNT.top, line unknown]:<br> The largest charge group contains 32 atoms.<br>
Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
There are: 2138 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for T-Coupling containing 7243 elements<br>Making dummy/rest group for Acceleration containing 7243 elements<br>
Making dummy/rest group for Freeze containing 7243 elements<br>Making dummy/rest group for Energy Mon. containing 7243 elements<br>Making dummy/rest group for VCM containing 7243 elements<br>Number of degrees of freedom in T-Coupling group rest is 15315.00<br>
Making dummy/rest group for User1 containing 7243 elements<br>Making dummy/rest group for User2 containing 7243 elements<br>Making dummy/rest group for XTC containing 7243 elements<br>Making dummy/rest group for Or. Res. Fit containing 7243 elements<br>
Making dummy/rest group for QMMM containing 7243 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>
<br>Checking consistency between energy and charge groups...<br><br>NOTE 2 [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>This run will generate roughly 2 Mb of data<br>writing run input file...<br><br>There were 2 notes<br><br>Back Off! I just backed up em.tpr to ./#em.tpr.2#<br><br>gcq#159: "Way to Go Dude" (Beavis and Butthead)<br>
<br>cunzhang@Debian:~/CNT$ mdrun -v -s em -e em -o em -c after_em<br>==help information==<br><br>Back Off! I just backed up md.log to ./#md.log.2#<br><br>Getting Loaded...<br>Reading file em.tpr, VERSION 4.0.5 (single precision)<br>
Loaded with Money<br><br><br>Back Off! I just backed up em.trr to ./#em.trr.2#<br><br>Back Off! I just backed up em.edr to ./#em.edr.2#<br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 1000<br>
Step= 0, Dmax= 1.0e-02 nm, Epot= -9.12531e+04 Fmax= 1.74309e+03, atom= 824<br>Step= 1, Dmax= 1.0e-02 nm, Epot= -9.30129e+04 Fmax= 8.17086e+03, atom= 802<br>Step= 3, Dmax= 6.0e-03 nm, Epot= -9.43526e+04 Fmax= 2.00407e+03, atom= 827<br>
Step= 5, Dmax= 3.6e-03 nm, Epot= -9.44415e+04 Fmax= 4.03472e+03, atom= 1<br>Step= 6, Dmax= 4.3e-03 nm, Epot= -9.47253e+04 Fmax= 3.99264e+03, atom= 802<br>Step= 8, Dmax= 2.6e-03 nm, Epot= -9.54446e+04 Fmax= 8.66104e+02, atom= 832<br>
<br>writing lowest energy coordinates.<br><br>Back Off! I just backed up after_em.gro to ./#after_em.gro.2#<br><br>Steepest Descents converged to Fmax < 1000 in 9 steps<br>Potential Energy = -9.5444641e+04<br>Maximum force = 8.6610358e+02 on atom 832<br>
Norm of force = 2.2713820e+02<br><br>gcq#247: "Let's Unzip And Let's Unfold" (Red Hot Chili Peppers)<br><br>cunzhang@Debian:~/CNT$ grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5<br><br>==help information==<br>
<br>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br>Replacing old mdp entry 'unconstrained-start' by 'continuation'<br>Ignoring obsolete mdp entry 'dihre-tau'<br>
Ignoring obsolete mdp entry 'nstdihreout'<br>Ignoring obsolete mdp entry 'nstcheckpoint'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<br>checking input for internal consistency...<br>processing topology...<br>
Opening library file /usr/share/gromacs/top/ffgmx.itp<br>Opening library file /usr/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/share/gromacs/top/ff_dum.itp<br>
Generated 1337 of the 1540 non-bonded parameter combinations<br>Opening library file /usr/share/gromacs/top/spce.itp<br>Excluding 3 bonded neighbours molecule type 'CNT'<br>Excluding 2 bonded neighbours molecule type 'SOL'<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><br><br>NOTE 1 [file CNT.top, line unknown]:<br>
The largest charge group contains 32 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br> groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>
Opening library file /usr/share/gromacs/top/aminoacids.dat<br>There are: 2138 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for Acceleration containing 7243 elements<br>
Making dummy/rest group for Freeze containing 7243 elements<br>Making dummy/rest group for Energy Mon. containing 7243 elements<br>Making dummy/rest group for VCM containing 7243 elements<br>Number of degrees of freedom in T-Coupling group System is 15315.00<br>
Making dummy/rest group for User1 containing 7243 elements<br>Making dummy/rest group for User2 containing 7243 elements<br>Making dummy/rest group for XTC containing 7243 elements<br>Making dummy/rest group for Or. Res. Fit containing 7243 elements<br>
Making dummy/rest group for QMMM containing 7243 elements<br>T-Coupling has 1 element(s): System<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>
<br>Checking consistency between energy and charge groups...<br><br>NOTE 2 [file grompp.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>This run will generate roughly 143 Mb of data<br>writing run input file...<br><br>There were 2 notes<br><br>Back Off! I just backed up pr.tpr to ./#pr.tpr.1#<br><br>gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije)<br>
<br>cunzhang@Debian:~/CNT$ mdrun -v -s pr -e pr -o pr -c after_pr<br>==help information==<br>Back Off! I just backed up md.log to ./#md.log.3#<br>Getting Loaded...<br>Reading file pr.tpr, VERSION 4.0.5 (single precision)<br>
Loaded with Money<br><br>There were 64 inconsistent shifts. Check your topology<br><br>Back Off! I just backed up pr.trr to ./#pr.trr.1#<br><br><br>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#<br><br>Back Off! I just backed up pr.edr to ./#pr.edr.1#<br>
starting mdrun 'Pure Water in water'<br>500000 steps, 250.0 ps.<br>There were 64 inconsistent shifts. Check your topology<br>step 0<br>t = 0.003 ps: Water molecule starting at atom 7226 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br><br>t = 0.004 ps: Water molecule starting at atom 7217 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>
<br>-------------------------------------------------------<br>Program mdrun, VERSION 4.0.5<br>Source code file: ../../../../src/mdlib/nsgrid.c, line: 357<br><br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>errors that give particles very high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.<br><br>Variable ci has value -2147483648. It should have been within [ 0 .. 200 ]<br>
<br>-------------------------------------------------------<br><br>"Right Now My Job is Eating These Doughnuts" (Bodycount)<br>
</div><br>Cun Zhang<br></div>