Example of how to create a solvated DNA MD simulation using LAMMPS starting with a pdb file

I’ve been over the LAMMPS web site and searched the web for an example or tutorial on how to set up a LAMMPS simulation of a solvated DNA system (starting with a pdb file) where all the residue, chain and sequence information (i.e. all the information in the ATOM/HETATM record) is retained in the output file. I have been unable to find such an example or tutorial.

I will be running the Kokkos GPU accelerated ReaxFF package.

Any help, tutorial links or examples would be appreciated.

Jim

James Kress Ph.D., President

The KressWorks® Institute

An IRS Approved 501 ©(3) Charitable, Nonprofit Corporation

Engineering The Cure” ©

(248) 573-5499

Learn More and Donate At:

Website: http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Institute/

Twitter: @KressWorksFnd

So the tools/ch2lmp scripts will convert a PDB file to a LAMMPS data file.

It also adds all the CHARMM ff coeff info and bond/angle topologies.

If you are wanting to run with ReaxFF, can you just delete

that info from the data file, and have what you need?

Steve

Steve,

Thanks. I’ll give it a try and let the List know what happens.

Jim

James Kress Ph.D., President

The KressWorks® Institute

An IRS Approved 501 ©(3) Charitable, Nonprofit Corporation

Engineering The Cure” ©

(248) 573-5499

Learn More and Donate At:

Website: http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Institute/

Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

One other thing you probably already realize.

The LAMMPS data file will just have atom IDs, types,

molecule IDs (all integers).

So if this:

all the information in the ATOM/HETATM record)

is text-based info like CHARMM atom types or residue

names, it will not be preserved by LAMMPS.

However, the ch2lmp tool also has a script which

converts LAMMPS dump snapshots back into CHARMM-

compatible files, PDB if I remember. That step may

re-associate the LAMMPS atom ID with the info in

the original PDB. Not sure if it will do what you are

asking precisely, but that is where to look …

Steve

That step may

re-associate the LAMMPS atom ID with the info in

the original PDB. Not sure if it will do what you are

asking precisely, but that is where to look …

Thanks. That is a concern that I will have to address. I need to be able to visualize (in VMD, for example) the results of the simulation within the context of the nucleic acid structure in the solvated system. If the atom type, residue and chain information corresponding to each atom is not retained, I will have to find a way to reclaim it.

I hope the ch2lmp tool will do this …

Jim

James Kress Ph.D., President

The KressWorks® Institute

An IRS Approved 501 ©(3) Charitable, Nonprofit Corporation

Engineering The Cure” ©

(248) 573-5499

Learn More and Donate At:

Website: http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Institute/

Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.