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Minimization, Normal modes, Monte Carlo,... Jump to new posts
Re: Surface Tension and NVT, NPAT Simulations rmv 04/19/21 11:04 PM
For my work, I've needed some of the newer OpenMM features not yet available in the CHARMM interface, esp. the new, more efficient Nose-Hoover thermostat with multiple heat baths (for Drude force fields), as was as the LJ-PME method for long range VDW. Fortunately, one of our former post-docs put together a python package (install required) that provides a single, simple python script that has all of the same information you would put in a CHARMM input script. I have had to improve my knowledge of python, which has been worth the effort.

I still use CHARMM for most analyses, using the DCD format files from OpenMM, and the same PSF I used to build the initial model with CHARMM.
9 111 Read More
Script Archive Jump to new posts
Re: getprop script rossi 04/13/21 05:00 PM
Rick,


I figured this out.

One value provides the AVERAGE surface tension after 1000 steps, and the second value provides the average fluctuation of the surface tension for the 1000 time steps. This is also the output given for other properties.

DUH!!!

Angelo
1 26 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Re: Infinte ELEC energy of Drude simulation rmv 04/12/21 03:53 PM
Please refer to the READ BEFORE POSTING topic for helpful hints, esp. for the use of .txt file attachments.

One possibility is a problem with the Drude conversion, or the initial relaxation of the Drude particles.
2 26 Read More
QM/MM Discussion and Questions Jump to new posts
QCHEM and umbrella sampling bnumn 04/09/21 08:08 PM
Does QCHEM have full compatibility with the RXNCOR module? I assumed it did, but I am conducting tests on a system that worked perfectly fine in the default QM/MM CHARMM module but with the QCHEM module, the structure just falls apart. I am puzzled why this might be the case. The QCHEM portion of my CHARMM input is:
Quote
QCHEM REMO NOGU COOR PARALLEL 22 OMP sele QMS end

Any suggestion would be appreciated.
0 23 Read More
Installation and Testing Jump to new posts
Re: Installing charmm45 with GAMESS-UK interface moth 04/01/21 07:41 AM
@milan I inherited version 7 from our group/lab when I joined. So I didn't have to contact CFS, which looks like the only listed way of getting the software now?

@rmv Yes, the tools I'm working on are unfortunately linked with GAMESS-UK (which might just mean we're doomed from the start), which is why I'm keen to get it included if possible. And these use PGI to compile, so as you point out I do need to compile CHARMM with PGI as well.

If the short answer is that pursuing GAMESS-UK with CHARMM is a bad idea (also considering the longer term) then that is also something useful to know.
6 149 Read More
CHARMM-GUI Jump to new posts
Re: Deprotonated LYR(Retinal+LYS) in CHARMM-GUI cqcqxq 03/29/21 01:39 PM
I'm so sorry! The ".ret" means ".rtf" file. That was a writing blunder.
Achieve this by above-mentioned references.
It's different from the LYR in toppar_all36_prot_retinol.str which makes every LYR protonated. However, LYR needs to be deprotonated at times.
It's developed by understanding the charmm ff and referring to literature. And it can be used in CHARMM-GUI with engineered residues option(PDB reader or Membrane Builder). You can get a deprotonated LYR when you upload "LYR.zip".
2 95 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Re: Can Charmm compute pi stacking interaction? lennart 03/26/21 03:25 PM
OK. The relevant aspect of the energies computed by CHARMM is that they should always be used in a relative sense, so you should always compute the difference wrt some reference state. This means that even though the energy values you compute are all positive, there may still be an attraction between the two rings, as long as there is a minimum in the energy surface. If I remember correctly the minimum conformation for two benzenes using the CHARMM energy function is where the edge of one interacts with the flat surface of the other (more or less).

There are also interactions within each ring, which are probably positive, but not important for the interaction between the rings. To avoid this complication you can use the interaction_energy command (energy.info).
4 134 Read More
CHARMM-GUI Jump to new posts
Re: triple bond between nucleotide and its modification rmv 03/26/21 12:47 AM
Questions about CHARMM-GUI functionality should probably be asked via the Contact page on their site.
3 72 Read More
QM/MM Discussion and Questions Jump to new posts
Re: CHARMM constrained QM/MM dynamics crashes sreeganb 03/25/21 06:44 AM
Thanks! That worked like a CHARMM! I just had to move the CONS HARM after reading the coordinates step.
2 205 Read More
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