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Parameter Set Discussion Jump to new posts
drude small molecule implementation Nikhil Maroli 02/17/24 07:57 PM
Hello everyone,,
Being a new member of CHARMM, sorry to have this dumb question.

Can someone can give me a initial suggestions on how i can add the drude parameters i have created for a small molecules and start the simulation? i have parameter files in str formate.
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Parameter Set Discussion Jump to new posts
pdb to psf and crd Victor NNN 02/15/24 08:17 PM
Hello, Charmm users!

I have a database of polymer chains that consists of 500 monomers (not all of them are nucleotides; I have monomers of polystyrene, polycarbonate, and other synthetic polymers). I installed a charmm package and Pycharmm. I could prepare the topology file in CHARMM36 using CHARMM-GUI, but is it possible to create psf and crd files using this force field automatically using charmm procedures or pycharmm without using the web server? Could you please suggest tutorials on how to create psf and crd files for non-standard files using charmm procedures?

Best wishes,
Victor
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Installation and Testing Jump to new posts
Re: Run c40b1 in parallel using MPI banban 02/13/24 11:24 PM
Did you ever get this working? I have the same issue, charmm is running multiple instances, one on each cpu...
20 19,113 Read More
Minimization, Normal modes, Monte Carlo,... Jump to new posts
Re: Monte Carlo in implicit solvent (GBMV) banban 02/12/24 05:21 PM
Have you used EFF1 with CHARMM's Monte Carlo? I am trying to setup an implicit membrane and solvent with it now, but I can not get it to work.
3 3,473 Read More
Parameter Set Discussion Jump to new posts
Re: IC table generation error placing alkyl H rmv 02/10/24 03:50 PM
Check the output log file for warning and error messages.

The HBUILD command is much better at placing H atoms. Add the following after IC BUILD:

COOR INIT SELE HYDROGEN END
HBUILD SELE HYDROGEN END


For viewing via VMD, PDB is not the best choice; write a .PSF and .COR file, and use those instead. With PDB, VMD draws bonds based on distance and not the actual CHARMM-defined topology.
1 77 Read More
General Chemistry Discussions Jump to new posts
Re: Analysis of Multiple Independent Trajectories lennart 02/01/24 09:55 AM
You can analyze multiple independent trajectories by adding the keyword NOCHECK to the trajectory specification , see dynamc.info
Clustering can be performed in several ways. There is a fairly general clustering tool in correl, see correl.info.
1 98 Read More
Parameter Set Discussion Jump to new posts
Oxygen mass in CHARMM36m July 2020 gianluca 02/01/24 03:57 AM
One of the changes for CHARMM36m July 2020 "Summary of changes in version C45/46, 2020/7" in toppar_all.history is:

1a) Incorrect oxygen masses changed to 15.99940

This was done for files top_all22_prot.rtf and top_all36_prot.rtf. I have two questions:

1) Files par_all36m_prot.prm and par_all22_prot.prm were not updated, they still have:

MASS -1 O 15.99900 ! carbonyl oxygen
MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid
MASS -1 OC 15.99900 ! carboxylate oxygen
MASS -1 OH1 15.99900 ! hydroxyl oxygen

Are the masses in the parameter files normally ignored and taken just from the topology files? Just curious why the masses are repeated in both the topology and parameter files. Would it be safer to correct the oxygen mass also in the parameter files?

2) The oxygen of H2O2 in toppar_water_ions.str still has the mass of 15.99900:
grep 15.99900 toppar_water_ions.str
MASS -1 OPER 15.99900 O ! O of H2O2
MASS -1 OPER 15.99900 ! O of H2O2

Should this also be 15.99940 for consistency?

Thanks!
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QM/MM Discussion and Questions Jump to new posts
Charge and Multiplicity in SCCDFTB Palani 01/29/24 09:19 PM
Dear All,
I am trying to minimize my ligand, hydroxyl group, and Zn(2+) ions using SCC-DFTB. While the QM/MM minimization the residues which are selected as QM region are broken. I have verified the net charge of my QM region, however I'm getting the same issue. My questions are,
1) How can I include the multiplicity in the SCC-DFTB input file?
2) What are the factors causing the QM residue to break?

The respective input and structure are attached here.
Please suggest me how to solve this issue.

Thank you.
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