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Molecular Dynamics Jump to new posts
Re: FEP output file? lennart 12/07/21 09:11 PM
You may want to address this question to GROMACS support, if it exists. This site is for CHARMM questions (perhaps the URL www.CHARMM.org/... is misleading?)
The scientific approach here is of course to produce the desired file yourself.
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Molecular Dynamics Jump to new posts
Re: FEP output file? rmv 12/07/21 05:36 PM
CHARMM has a variety of methods for FEP so you may need to be more specific, although I'm not sure how much any of them would help with a GROMACS issue.
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Molecular Dynamics Jump to new posts
FEP output file? cg_nanome 12/07/21 04:52 PM
We're working on a GROMACS integration and would like to be able to support FEP files types. Does anyone have an FEP output file they would be willing to share for testing purposes only? (It will not be published or used in any other way). Thanks.
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal jamesmao 12/07/21 03:22 PM
Hi Lennart, what do you mean "very basic PBC"? do you mean the geometry of the box? thanks.
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Installation and Testing Jump to new posts
Re: 44b1 source code question rmv 12/06/21 09:53 PM
For information on obtaining CHARMM source code, see this page
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Installation and Testing Jump to new posts
44b1 source code question Jeff Polasek 12/06/21 09:42 PM
Howdy,

I support a group that uses CHARMM. The group needs to perform some additional calculations on a project that used CHARMM 44b1. We need to re-compile this version, but do not have the source code.

What is the best way to get the source code for this version?

Thanks
Jeff
--
Jeff Polasek
Sr. IT Pro I
College of Engineeing
Texas A&M University
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal lennart 11/29/21 06:29 PM
COOR ANAL only supports very basic PBC. An alternative approach is to preprocess the trajectory and recenter each frame with the site of interest at the center. COOR MERGE RECENTER.
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal rmv 11/28/21 09:30 PM
If the site can be near a unit cell boundary, then you should use PBC or else under-counting can occur.

The HIST feature of COOR DISTance can be used to compute g(r) in a loop over frames, but it is much less efficient than using COOR ANAL and not recommended for general use. The COOR DIST approach does offer greater flexibility, including the ability to process each frame before accumulating histogram data, but is more cumbersome to use and significantly slower.
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal jamesmao 11/27/21 11:20 PM
Since I only need local rdf around a specific site, I did not try PBC. Will give it a try later. BTW, what are other options/modules for rdf analysis in charmm besides coor anal? thanks.
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal lennart 11/23/21 07:22 PM
Good! Honest mistake, rather. As long as you don't repeat it and expect a different outcome you're OK, loosely quoting A. Einstein (a physicist of some fame a hundred years ago).
Having written parts of the underlying code, and used it a lot, I would like to point out that coor anal is not quite as bad as it may sound.
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal jamesmao 11/22/21 07:01 PM
thanks Lennart. Turns out I made a silly mistake: 100ns is 100000000 instead of 10000000!
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Setup, I/O, and Basic questions Jump to new posts
Re: rdf using coor anal lennart 11/22/21 05:13 PM
Strange, the partial rdfs should sum up to the overall, as you expect. One thing that could confuse the issue is periodic boundary conditions, in particular for something like ions that I assume are spread out all over you system. COOR ANAL can handle some basic PBCs, but your command does not request this.
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Setup, I/O, and Basic questions Jump to new posts
rdf using coor anal jamesmao 11/22/21 03:05 AM
I am trying to study rdf of my system. My script is something like this:

coor anal select type ION end -
xref @xsite yref @ysite zref @zsite -
firstu 51 nunit 1 begin ?start skip ?skip -
isdist 41 -
rsph 999.9 mgn 800 dr 0.2 -
dens 0.001

The trajectory file contains 500ns data. I also run the script for every 100ns data by assigning the "begin" and "stop" in the third line such as "firstu 51 nunit 1 begin 10000000 stop 20000000 skip ?skip -".
I thought the rdf using all 500ns should be the average of the five 100ns rdf. However, although the five 100ns rdf plots are similar, their average is very different from the 500ns one. I even see a peak not present in any of the 100ns plots appears in the 500ns plot (within r<1). I am quite confused. Can anyone give me some hint? isn't rdf the average of rdf from each frame?

thank you very much.
james
7 232 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: generating peptide from sequence rmv 11/18/21 02:56 PM
Have you tried the Script Archive forum at this site?

See also charmmtutorial.org
1 87 Read More
Setup, I/O, and Basic questions Jump to new posts
generating peptide from sequence cm14sjm 11/18/21 12:47 PM
Hello, how do I generate a new peptide without a PDB, in a linear conformation from its amino acid sequence? It has been a few years since I did this and I no longer have the input file, but I remember something like GENERATE PEPT 5 ALA ALA ALA etc. Also, once I have that command how do I simulate that peptide, do I just go ahead into the DYNA section or do I need to write a PDB first? I have tried googling it but found nothing.


Thanks a lot!
1 87 Read More
Parameter Set Discussion Jump to new posts
N-methylated amino acid parameters ncf0003 11/15/21 04:16 PM
Hello!

I was wondering if Kenno was still the person to contact for the N-methylated parameters for charmm36 (https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=35092). I figured since he left the lab he might have passed them off.
0 63 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: IC Edit not modifying coordinates Anmol 11/10/21 02:26 AM
Thanks for your reply. The same script works now. As you pointed out, the dihedral mentioned had wrong atom order, thus was not part of existing IC and was not being used to generate the coordinates.
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Setup, I/O, and Basic questions Jump to new posts
Re: IC Edit not modifying coordinates rmv 11/09/21 03:21 PM
The script is not sufficient for diagnosis; there are probably some major hints in the output log file and .pdb files.

For changing a dihedral via IC EDIT, COOR INIT, and IC BUILD, one way is to apply COOR INIT to all atoms on only one side of the dihedral, e.g. N1, C3, and all of atoms connected to those atoms. For a small molecule, you could probably use COOR INIT on all of the atoms. Also, there could be issues if the 4 atoms listed in IC EDIT are not already part of an existing IC entry from the topology file.
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Setup, I/O, and Basic questions Jump to new posts
IC Edit not modifying coordinates Anmol 11/09/21 06:36 AM
I am trying to change a particular dihedral for a known set of coordinates by editing the IC. The IC changes but coordinate remains the same.
I could not figure out the mistake in following code.

Code
stream toppar.str
stream @str
set residue @resi

read sequence @resi 1
generate @resi first none last none setup warn

read coor card name @resicrd

ic fill ! preserve

set value -180

label repeat
ic edit
  dihedral 1 N1 1 C3 1 C4 1 C5 @value
end
ic print
coor init sele (type N1 .or. type C3 or. type C4 .or. type C5) end
ic build

open unit 30 write form name @resi_@value.pdb
write coor pdb unit 30
close unit 30
incr value by 15
if @value eq 180 then
   stop
else
   goto repeat
endif

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