Hello,
I am trying to use the rerun option with an xtc file (written with lammps). I haven’t seen any post about this, so I wanted to make sure this is even possible. I understand this has to be done through the molfile option:
rerun input.xtc dump x y z format molfile xtc
I tried giving it the path to the molfile plugin directory, which didn’t help.
In such case - which plugin do I need to include in my vmd installation? I found only this mention of the relevant plugin, but found it nowhere else:
https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/trrplugin.html
Thank you,
Liel Sapir
Postdoctoral associate
Duke University
What is the exact error message you get and what are your exact LAMMPS and VMD versions in use?
Axel.
Hi Axel,
Thank you for your response!
The error I get is:
ERROR: Unknown dump reader style (…/read_dump.cpp:211)
I am using LAMMPS/16Mar18 and VMD 1.9.4
Thanks,
Liel
You didn’t mention what OS/Platform you are using. I will assume Linux.
You cannot have VMD version 1.9.4 because it has not been released. There are only (numbered) alpha test versions.
And while using a (newer) alpha version of VMD, you are using a rather old version of LAMMPS (over 2 years). That version of LAMMPS will, by default, be compatible with plugins from VMD before version 1.9.3. The copy of the VMD include defining the VMD plugin ABI version was updated in newer LAMMPS versions, but if you are using a VMD alpha version, you need to use the vmd plugin header that matches your VMD plugins. You don’t need to provide a name to a specific plugin, but the path to a folder and then the code in LAMMPS will try to open all available plugins and find a match.
The error message, however, indicates that your LAMMPS executable doesn’t even have support for the USER-MOLFILE package included. So it is not about the plugin but about support for USER-MOLFILE.
with all that information i would suggest the following:
- update your LAMMPS version. you get lots of new features and many bugfixes as a bonus
- make sure you include/enable the USER-MOLFILE package when building LAMMPS and also update the VMD headers from your VMD installation (<VMD_LIB_DIR>/plugins/include) or point the LAMMPS compilation to that folder
- either copy the gromacsplugin.so to your working directory or use the path to your folder with the VMD plugins in the rerun command
Please note, that the xtc plugin will not store and read image flags, so if you didn’t write out unwrapped coordinates, you may get some warnings and unexpected results for molecular systems.
Axel.
Hi Axel,
Thank you for your help! Indeed I use Linux. Our system admin followed your suggestions and I’m able to rerun the xtc file now without errors.
About your last comment - I indeed wrote unwrapped coordinates to the xtc file (by using “dump_modify 1 unwrap yes”).
I assumed using “wrapped no” in the rerun command would take care of the periodic boundaries. Is that correct?
Thank you for your help,
Liel
About your last comment - I indeed wrote unwrapped coordinates to the xtc file (by using “dump_modify 1 unwrap yes”).
I assumed using “wrapped no” in the rerun command would take care of the periodic boundaries. Is that correct?
yes. regardless. I would recommend to make a simple test and use rerun with the exact same settings of the original run and compare energies and pressure for a few frames. since xtc is a lossy compression format, you cannot expect a perfect match, but it should agree within reason.
that way it is simple to confirm, that your rerun setup is correct, and then you can change it any which way you like.
axel.
Hi Axel,
OK great, thank you so much for your help!
Best,
Liel