ERROR on proc 3: Bond atoms 58972 58979 missing on proc 3 at step 1

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1

Dear all
I meet the error: Bond atoms 58972 58979 missing on proc 3 at step 1 or error: Out of range atoms - cannot compute PPPM. ​
I have try to adjust the timestep , box size but they didn’t work. I also tried to simulate toluene and water separately and found that it worked well.
Below is my infile and error message. Does anyone can tell me why I get this error?

echo screen

units real

atom_style full

dimension 3

boundary p p f

#newton on

bond_style harmonic

angle_style harmonic

dihedral_style opls

improper_style harmonic

global model settings

variable rhoc7h8 equal 8.905

variable rhoh2o equal 4.931

variable t equal 293.15

region box block 0.001 80 0.001 80 -1.001 161.0 units box
create_box 7 box &

bond/types 5 &

angle/types 6 &

dihedral/types 7 &

improper/types 1 &

extra/bond/per/atom 4 &

extra/angle/per/atom 10 &

extra/dihedral/per/atom 18 &

extra/improper/per/atom 9 &

extra/special/per/atom 12
molecule toluenemol toluene-molecule.txt

molecule h2omol H2Ospce.mol

#wall region

region lower block INF INF INF INF INF 0.0

region upper block INF INF INF INF 160.0 INF
#liquid 1 region

region water block 0 80 0 80 0 80 units box side in

#liquid 2 region

region toluene block 0 80 0 80 80 160 units box side in

##creat atoms

water atoms

lattice fcc ${rhoh2o}

create_atoms 0 region water mol h2omol 2345 units box

toluene atoms

lattice fcc ${rhoc7h8}

delete_atoms region toluene mol yes compress yes

create_atoms 0 region toluene mol toluenemol 1234 units box
#wall atoms

lattice fcc 10

delete_atoms region lower mol yes compress yes

create_atoms 7 region lower units box

create_atoms 7 region upper units box

##mass

mass 1*2 12.011 #C

mass 3*5 1.008 #H

mass 6 15.999 #O

mass 7 1.0

MD init settings

group c7h8 type 1 2 3 4

group h2o type 5 6

group lower region lower

group upper region upper

group wall union lower upper

group wall type 7

group flow union c7h8 h2o

2

Dear all
I meet the error: Bond atoms 58972 58979 missing on proc 3 at step 1 or error: Out of range atoms - cannot compute PPPM.
I have try to adjust the timestep , box size but they didn’t work. I also tried to simulate toluene and water separately and found that it worked well.
Below is my infile and error message. Does anyone can tell me why I get this error?

the most common reasons are incorrect or incompatible force field settings or a bad initial geometry with overlapping atoms.

axel.

3

Hi axel, thanks very much.
I simulated individual toluene, and individual water , they can work well. dose it mean that the force field is ok ?

4

Hi axel, thanks very much.
I simulated individual toluene, and individual water , they can work well. dose it mean that the force field is ok ?

no. this only tests the interaction of the same part with itself. it does not validate the interactions between toluene and water.

axel.

5

thanks very much，axel.

My force field is generated from moltemplate , they are all oplsaa force field. I think the force field is no problem.

And when I adjust, I get another error , Non-numeric positions - simulation unstable. the error : Bond atoms missing on proc 3 at step 1 and error: Out of range atoms - cannot compute PPPM. The three errors were reversed .
I have no direction to change. Who can give me some advice ? thanks very much !

da

6

thanks very much，axel.

My force field is generated from moltemplate , they are all oplsaa force field. I think the force field is no problem.

we just recently had a case being discussed on this mailing list where moltemplate would not correctly assign all(!) force field parameters for OPLS/AA.

And when I adjust, I get another error , Non-numeric positions - simulation unstable. the error : Bond atoms missing on proc 3 at step 1 and error: Out of range atoms - cannot compute PPPM. The three errors were reversed .
I have no direction to change. Who can give me some advice ? thanks very much !

you have not addressed the second common possibility of causing this kind of error: close contacts.

axel.

7

hi axel and others
I used the fix nve/limit and delete_atoms overlap to push the overlap atoms , it can run .but the temperature oscillation is particularly large.
Step TotEng Temp Volume Press Density

0 60096.382 292.2887 1069515.2 3741.577 1.3100191

500 60095.843 262.91919 1069515.2 2981.8664 1.3100191

1000 60100.085 219.47043 1069515.2 1833.7011 1.3100191

1500 60103.64 214.5884 1069515.2 1700.4782 1.3100191

2000 60109.565 220.18461 1069515.2 1931.2933 1.3100191

2500 60115.098 195.55632 1069515.2 1514.1802 1.3100191

3000 60121.63 166.9188 1069515.2 1113.0862 1.3100191

3500 60128.179 167.234 1069515.2 1525.8216 1.3100191

4000 60134.834 172.38895 1069515.2 2014.5108 1.3100191

4500 60142.38 161.73207 1069515.2 1875.4798 1.3100191

5000 60152.178 165.90968 1069515.2 1811.7448 1.3100191

5500 60162.908 196.5491 1069515.2 2208.3022 1.3100191

6000 60176.032 207.60565 1069515.2 2010.8681 1.3100191

6500 60187.713 180.45717 1069515.2 799.78595 1.3100191

7000 60202.312 165.53578 1069515.2 -35.541022 1.3100191

7500 60216.007 191.15602 1069515.2 412.40143 1.3100191

8000 60234.13 212.57883 1069515.2 1101.0483 1.3100191

8500 60252.073 195.89785 1069515.2 1085.869 1.3100191

9000 60268.473 174.30401 1069515.2 1114.9153 1.3100191

9500 60286.079 179.52335 1069515.2 1954.2531 1.3100191

10000 60303.52 189.91204 1069515.2 2919.1479 1.3100191

this is why? what is wrong whit it

8

please look at the density. that looks very high for the compounds you are simulating. doesn’t this bother you?

fluctuations are are normal during MD simulations. their magnitude depends on several factors. so the question is whether they are too large or not. impossible to say from remote. also, since you now do get a trajectory, you should visualize it and see what is going on, especially around the steps when the temperature jumps.

for molecular systems, the method using (temporarily) a soft potential and fix adapt to unoverlap the system - like in the micelle example input - may work better than delete_atoms and fix nve/limit.

axel.

9

thanks very much for your suggestions, axle. I will try to do it .

10

hello, alex

Sorry to trouble you again, i found that whether it is t fix nve/limit or soft and fix adapt to unoverlap atoms, it will run for a period of time before the atom is missng again. that is way? I felt very distressed.
Look forward to your reply, thanks very much!

200 79570 249.35123 1036858.9 1521.4038 0.93346602
ERROR on proc 0: Shake atoms 112 113 114 missing on proc 0 at step 222

11

hello, alex

Sorry to trouble you again, i found that whether it is t fix nve/limit or soft and fix adapt to unoverlap atoms, it will run for a period of time before the atom is missng again. that is way? I felt very distressed.
Look forward to your reply, thanks very much!

we are going in circles now. i can only repeat what i have stated before. and you have NOT provided any convincing evidence that a) you did the unoverlapping procedure properly and successfully, b) you properly addressed the extreme high potential energy and pressure and abnormal density (which are most likely connected), c) that your force field parameter assignment and topology data is accurate and consistent, d) that your simulation parameters are suitable for the system that you want to simulate.

there is not much else that i can do from remote. you are making your own life miserable by looking for a “quick fix” rather than addressing the situation systematically and working towards a solution in an incremental fashion. teaching you how to manage your work and how to address problems is beyond the scope of this mailing list.

axel.

12

thanks very much， axel.
I have tested a small number of molecules on the system and found it can smoth work . But once I add more toluene molecular, it’s going to make an error (bond atoms missing ). I think it should be able to identify the problem of atomic overlap.
In addition, I replaced ij/cut/coul/long with soft interaction to push overlap atoms and found that it worked fine initially, but after running a few steps, UNfix fixadapt. Running the interaction as ij/cut/coul/long still reports an error (bond atoms missing). Is it because I failed to push away the overlapping atoms ?

13

thanks very much， axel.
I have tested a small number of molecules on the system and found it can smoth work . But once I add more toluene molecular, it’s going to make an error (bond atoms missing ). I think it should be able to identify the problem of atomic overlap.

you are (again) limiting the possible solutions by making assumptions and jumping to conclusions. it can or cannot be due to atom overlap. it can also be due to force field issues or missing constraints or incorrect simulation settings. so the only way to move forward is to isolate the situation where the simulation cannot run stable and then carefully look at all possible causes. visualization and dumping position and thermo data frequently is the most important tool for that.

In addition, I replaced ij/cut/coul/long with soft interaction to push overlap atoms and found that it worked fine initially, but after running a few steps, UNfix fixadapt. Running the interaction as ij/cut/coul/long still reports an error (bond atoms missing). Is it because I failed to push away the overlapping atoms ?

how on earth should i know? perhaps you didn’t do the unoverlapping properly (e.g. by increasing the soft potential to rapidly and/or taking too little simulation time to do this step.). …and as mentioned now multiple times before, you have not provided proof that your force field setting is correct. so if the unoverlapping works properly, but the force field doesn’t, you can get what you describe. but i cannot know this from remote.

as you may have noticed, this discussion is now going completely in circles. i have nothing to add and end up repeating what i have already stated. so unless you have something substantially new to report, i will not respond anymore.

axel.

14

thanks very much， axel.
I did not simply look for the cause through the fix command. Many of the intermediate details are not mentioned. I’m sorry I had a problem with my presentation
The density was adjusted, and there was an atomic type that did not correspond to the density. In addition, my model can normally run to balance by deleteoverlap where cutoff=1.5 or above, and the energy pressure is in the normal range. It can also be found through visualization that it can form a two-phase interface, but too many toluene molecules are deleted, which is not what I want. But this at least shows that I have no problem setting the force field.
Next, I’ll model and optimize toluene water separately, and then put them together with write_date and read_date commands. I think the overlap problem will be much better.