segmentation fault(core dumped) error for complex mixture

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1

Dear Friends,

I am trying to run my script on the Cluster but it shows “segmentation fault”.

The data file was created by using VMD and I did not find missing parameters, which is attached.

The attached script is to relax the system by increasing temperature. I used OPLS-AA force field. I tried to reduce timestep and it did not work.

The cluster is a parallel lammps platform. I have tried to use both versions of 2013 and 2014, one processor.

Can anyone try my data and script? I will appreciate it if you provide any suggestions!

Thanks!

Jane

data.mixture (166 KB)

in.mixturenvt (610 Bytes)

2

Dear Friends,

I am trying to run my script on the Cluster but it shows "segmentation
fault".

The data file was created by using VMD and I did not find missing
parameters, which is attached.

have you visualized your input? you have multiple molecules on top of
each other and passing through each other.

The attached script is to relax the system by increasing temperature. I used
OPLS-AA force field. I tried to reduce timestep and it did not work.

no input file scripts can help with a bad starting geometry.

3

Thanks! Axel.

Yes, I also suspect the configuration. I can create the configuration of each component and it can work. But after combining with other components in VMD, it seems it does not work.

Do you have suggestion about how to build right configuration for my case?

Thanks!

Jane

4

Thanks! Axel.

Yes, I also suspect the configuration. I can create the configuration of
each component and it can work. But after combining with other components in
VMD, it seems it does not work.

Do you have suggestion about how to build right configuration for my case?

there are multiple ways. you can use VMD scripting to displace atoms
before you merge them. you can use a soft potential with fix adapt to
unoverlap the atoms. there should be examples for that in the mailing
list archives.

axel.