Thank you, Justin ! I have add the output generated by grompp and mdrun at the end.
> Cun Zhang wrote: > > hi, Justin. Thank you for your patience ! > > > > I'm still in trouble with infinite CNT simulation. > > > > I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A) > > with 832 atoms and water. I'm using x2top to generate the CNT.itp with > > share-bonds. The idea is that I generate a (16,0) CNT(CNT_B) with 960 > > atoms ( more 4 layer than CNT_A. Each layer has 32 atoms ). > > When I use CNT.itp generated by CNT_A and x2top, it works. But when I > > use the CNT.itp which has share-bonds information, it can't work. > > > > > > The process I'm doing CNT simulation is as follows: > > # the CNT_new.pdb is a (16,0) CNT with 960 atoms. > > # I add the custom forcefield parameters to tmp.top, and change the > > number of a charge group to 32, then rename it CNT.itp at the end. > > > > x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name > > CNT > > > > bash sharebond_script # create share bonds > > > > The script below is renumbering and removing atoms. Why are you doing > this? I > thought the purpose of CNT_new was to generate a larger structure? > 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. 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' ). 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. > > editconf -f CNT.pdb -o -box 3.8 3.8 5.614 > > > > Now you are manipulating CNT.pdb - is this the correct next step? If this > actually pertains to CNT_new.pdb, then the box size is insufficient to hold > the > larger structure. But now I'm just confused as to what you're doing. > This is the information when I run this command. I think it's ok. system size : 1.270 1.270 5.472 (nm) center : -0.000 0.000 2.736 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 1.900 1.900 0.071 (nm) new center : 1.900 1.900 2.807 (nm) new box vectors : 3.800 3.800 5.614 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 81.07 (nm^3) > > genbox -cp out -cs -p CNT -o b4em.pdb #The simulation box size can be > > > seen in b4em.pdb > > > > pymol b4em.pdb #remove water. After editing it,I save it as b4em.pdb > > too.Now the information about box size is losing. I don't know why.I'm > > not familar with it :) > > > > editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information > > about box size > > vim CNT.top #change the number of water to make it the same as > b4em.pdb > > grompp -f em -o em -c b4em -p CNT -maxwarn 5 > > mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em > > Does energy minimization work? What did the potential energy and maximum > force > converge to? Again, what is the purpose of "-maxwarn 5"? Are there errors > that > grompp is generating that you are simply trying to bypass? This is > generally a > bad idea. > Yes, EM work. Steepest Descents converged to Fmax < 1000 in 9 steps Potential Energy = -9.5444641e+04 Maximum force = 8.6610358e+02 on atom 832 Norm of force = 2.2713820e+02 There are two notes,no warnings,no errors when grompp. When I run the MD,errors come: 500000 steps, 250.0 ps. There were 64 inconsistent shifts. Check your topology step 0 t = 0.003 ps: Water molecule starting at atom 7226 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates t = 0.004 ps: Water molecule starting at atom 7217 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: ../../../../src/mdlib/nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 200 ] The output of grompp and mdrun are there. cunzh...@debian:~/CNT$ grompp -f em -o em -c b4em -p CNT -maxwarn 5 ==help information== Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ffgmx.itp Opening library file /usr/share/gromacs/top/ffgmxnb.itp Opening library file /usr/share/gromacs/top/ffgmxbon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 1337 of the 1540 non-bonded parameter combinations Opening library file /usr/share/gromacs/top/spce.itp Excluding 3 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... NOTE 1 [file CNT.top, line unknown]: The largest charge group contains 32 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 2138 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... Making dummy/rest group for T-Coupling containing 7243 elements Making dummy/rest group for Acceleration containing 7243 elements Making dummy/rest group for Freeze containing 7243 elements Making dummy/rest group for Energy Mon. containing 7243 elements Making dummy/rest group for VCM containing 7243 elements Number of degrees of freedom in T-Coupling group rest is 15315.00 Making dummy/rest group for User1 containing 7243 elements Making dummy/rest group for User2 containing 7243 elements Making dummy/rest group for XTC containing 7243 elements Making dummy/rest group for Or. Res. Fit containing 7243 elements Making dummy/rest group for QMMM containing 7243 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... NOTE 2 [file em.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 2 Mb of data writing run input file... There were 2 notes Back Off! I just backed up em.tpr to ./#em.tpr.2# gcq#159: "Way to Go Dude" (Beavis and Butthead) cunzh...@debian:~/CNT$ mdrun -v -s em -e em -o em -c after_em ==help information== Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file em.tpr, VERSION 4.0.5 (single precision) Loaded with Money Back Off! I just backed up em.trr to ./#em.trr.2# Back Off! I just backed up em.edr to ./#em.edr.2# Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 Step= 0, Dmax= 1.0e-02 nm, Epot= -9.12531e+04 Fmax= 1.74309e+03, atom= 824 Step= 1, Dmax= 1.0e-02 nm, Epot= -9.30129e+04 Fmax= 8.17086e+03, atom= 802 Step= 3, Dmax= 6.0e-03 nm, Epot= -9.43526e+04 Fmax= 2.00407e+03, atom= 827 Step= 5, Dmax= 3.6e-03 nm, Epot= -9.44415e+04 Fmax= 4.03472e+03, atom= 1 Step= 6, Dmax= 4.3e-03 nm, Epot= -9.47253e+04 Fmax= 3.99264e+03, atom= 802 Step= 8, Dmax= 2.6e-03 nm, Epot= -9.54446e+04 Fmax= 8.66104e+02, atom= 832 writing lowest energy coordinates. Back Off! I just backed up after_em.gro to ./#after_em.gro.2# Steepest Descents converged to Fmax < 1000 in 9 steps Potential Energy = -9.5444641e+04 Maximum force = 8.6610358e+02 on atom 832 Norm of force = 2.2713820e+02 gcq#247: "Let's Unzip And Let's Unfold" (Red Hot Chili Peppers) cunzh...@debian:~/CNT$ grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5 ==help information== Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Replacing old mdp entry 'unconstrained-start' by 'continuation' Ignoring obsolete mdp entry 'dihre-tau' Ignoring obsolete mdp entry 'nstdihreout' Ignoring obsolete mdp entry 'nstcheckpoint' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ffgmx.itp Opening library file /usr/share/gromacs/top/ffgmxnb.itp Opening library file /usr/share/gromacs/top/ffgmxbon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 1337 of the 1540 non-bonded parameter combinations Opening library file /usr/share/gromacs/top/spce.itp Excluding 3 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... NOTE 1 [file CNT.top, line unknown]: The largest charge group contains 32 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. initialising group options... processing index file... Analysing residue names: Opening library file /usr/share/gromacs/top/aminoacids.dat There are: 2138 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... Making dummy/rest group for Acceleration containing 7243 elements Making dummy/rest group for Freeze containing 7243 elements Making dummy/rest group for Energy Mon. containing 7243 elements Making dummy/rest group for VCM containing 7243 elements Number of degrees of freedom in T-Coupling group System is 15315.00 Making dummy/rest group for User1 containing 7243 elements Making dummy/rest group for User2 containing 7243 elements Making dummy/rest group for XTC containing 7243 elements Making dummy/rest group for Or. Res. Fit containing 7243 elements Making dummy/rest group for QMMM containing 7243 elements T-Coupling has 1 element(s): System Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... NOTE 2 [file grompp.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 143 Mb of data writing run input file... There were 2 notes Back Off! I just backed up pr.tpr to ./#pr.tpr.1# gcq#97: "The Universe is Somewhere In Here" (J.G.E.M. Fraaije) cunzh...@debian:~/CNT$ mdrun -v -s pr -e pr -o pr -c after_pr ==help information== Back Off! I just backed up md.log to ./#md.log.3# Getting Loaded... Reading file pr.tpr, VERSION 4.0.5 (single precision) Loaded with Money There were 64 inconsistent shifts. Check your topology Back Off! I just backed up pr.trr to ./#pr.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up pr.edr to ./#pr.edr.1# starting mdrun 'Pure Water in water' 500000 steps, 250.0 ps. There were 64 inconsistent shifts. Check your topology step 0 t = 0.003 ps: Water molecule starting at atom 7226 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates t = 0.004 ps: Water molecule starting at atom 7217 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates ------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: ../../../../src/mdlib/nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 200 ] ------------------------------------------------------- "Right Now My Job is Eating These Doughnuts" (Bodycount) Cun Zhang
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