VMD-L Mailing List

From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Thu Jun 10 2021 - 11:11:59 CDT

Hi,
This problem is probably due to water molecules near acyl chains moving out
of the hydrophobic region. One possible solution is, during system
construction, make the water box in the XY axis at least 10 angstroms
smaller than the lipid bilayer in both positive & negative direction. You
can increase the thickness of the water box in z direction to compensate.
During npt equilibration pbc systems will merge to give a good protein
bilayer system. This worked with my system, hopefully will work
within yours too.

On Thu, 10 Jun 2021, 21:26 Vermaas, Josh, <vermaasj_at_msu.edu> wrote:

> Which atom is fast? The NAMD log will tell you. That is where you start
> looking.
>
>
>
> -Josh
>
>
>
> *From: *"Ropon-Palacios G." <groponp_at_gmail.com>
> *Date: *Thursday, June 10, 2021 at 11:19 AM
> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>, Chris Neale <candrewn_at_gmail.com>,
> vmd-L <vmd-l_at_ks.uiuc.edu>
> *Subject: *Found bad contact
>
>
>
> Dear vmd users,
>
>
>
> How can i found bad conctacts?, I’ve create protein-membrane system with
> charm-gui I’m try minimize system but always have problem with “atoms
> moving too very fast”, try use several protocols of minimization but not
> can fix it. Them want found bad contact or clashes.
>
>
>
> Please suggest me a script for it.
>
>
>
> Best.
>
>
>
> --
>
> *Ropón-Palacios G. BSc., MSc. *
>
> Computational biophysicist,
>
> Associate Research,
>
> Laboratorio de Modelagem Computacional,
>
> Departamento de Ciências Exatas,
>
> Universidad Federal de Alfenas, Minas Gerais, Brasil.
>
> Phone: +51 935 055240.
>
> E-mail: groponp_at_gmail.com.
>
>
>
>
>
>
>
>
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of "Vermaas, Josh" <
> vermaasj_at_msu.edu>
> *Date: *Thursday, June 10, 2021 at 9:56 AM
> *To: *Chris Neale <candrewn_at_gmail.com>, vmd-L <vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: loading multiple different topologies into the same
> "molecule"
>
>
>
> Hi Chris,
>
>
>
> Can’t you use topotools mergemols to do this?
>
>
>
> package require topotools
>
> set pdblist [glob *pdb]
>
> set midlist [list ]
>
> foreach pdb $pdblist {
>
> set mid [mol new $pdb]
>
> lappend midlist $mid
>
> }
>
> set mol [::TopoTools::mergemols $midlist]
>
> animate write psf merged.psf $mol
>
> animate write pdb merged.pdb $mol
>
>
>
> This would get you everything into a single molecule, but as you state,
> this would be a royal mess to select over. What exactly are you trying to
> do that needs them in the same molecule?
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Chris Neale <
> candrewn_at_gmail.com>
> *Date: *Wednesday, June 9, 2021 at 8:32 PM
> *To: *vmd-L <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: loading multiple different topologies into the same
> "molecule"
>
>
>
> Dear users:
>
>
>
> does anybody know if it's possible to load many different PDB files into
> the same molecule and have those PDB files have different system
> compositions? An example would be to be able to run "vmd -f *.pdb" on a
> large collection of PDB files of the same protein family, etc. I realize
> that some selection tools would then break (e.g., a selection of "resid 19"
> might not always play nice), but sensible selections, like "protein"
> "water", etc might be OK. I know that there are some good ideas with
> putting particles far away for things like constant pH simulations, but
> that's not as generalizable as loading in all SH2 domains in the PDB, for
> example.
>
>
>
> I realize that I could script image generation, or load hundreds of
> separate molecules with a "vmd -m *pdb" command, but none of those is as
> intuitive for browsing structural data where some models may have missing
> residues, insertions, different sequences, different numbers of water, etc.
>
>
>
> If such a capability does not exist, can anyone guess how hard it would be
> to implement right in the GUI? I'm not asking for anyone to actually do
> this, just trying to get a sense of how hard it would be.
>
>
>
> PS: I've got 10+ years experience with VMD, and I'm fairly confident that
> this is not possible at the present time. However, I'm asking since (a)
> somebody might have a great alternative solution and (b) in any event I'm
> interested in learning how hard this would be to implement.
>
>
>
> Thank you for your advice,
>
> Chris.
> 

-- 
Diship Srivastava
JRF
Department of Chemistry
IIT(ISM) - Dhanbad
India