VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 21 2022 - 06:07:54 CDT

Do you have spaces in the path? If so, try enclosing the path in
double-quotes, i.e. "/path/to/....".

Giacomo

On Tue, Jun 21, 2022 at 6:12 AM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hi,
>
> Thank you so much for your help. The commands in the Tk console worked
> perfectly.
>
> I would like to put those commands in a .vmd file to be able to use source
> file.vmd to run all the commands rather than typing them each time. Is
> there a way to add a .vmd file to the path so that if I am not in the
> directory holding the .vmd file it will still run?
>
> I created the .vmd file and placed it in my VMD folder. When I am creating
> the pdb/psf files without water, I change to my desired directory in the Tk
> console and then would like to run the .vmd file. However, since the .vmd
> file is not in the directory I changed into, I get an error that no file
> can be found. I also tried running source /path/to/file.vmd, but I get this
> error: wrong # args: should be "source ?-encoding name? fileName".
>
> Best,
> Christos
> ------------------------------
> *From:* Geist, Norman <norman.geist_at_uni-greifswald.de>
> *Sent:* Sunday, June 19, 2022 9:51 PM
> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>; Axel
> Kohlmeyer <akohlmey_at_gmail.com>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: How to reduce the size of a .dcd file?
>
> Hi,
>
> saving a shortened DCD is also quite easily possible. Load PSF and PDB
> (PSF 1st.) and then in Extensions->TKConsole:
>
> set a [atomselect top "not water"]
> $a writepsf short.psf
> $a writepdb short.pdb
>
> Saving the indexfile for catdcd is similarly easy:
>
> set fp [open indexfile w}]
> set a [atomselect top "not water"]
> puts $fp [$a get serial]
> $a delete
> close $fp
>
> Then use catdcd like:
>
> catdcd -s short.pdb -o short.dcd -otype dcd -i indexfile -dcd long1.dcd
> -dcd long2.dcd
>
> Bests
> Norman Geist
>
>
> Am Sonntag, den 19-06-2022 um 15:15 schrieb Efthymiou, Christos:
>
> Thank you for the link to the Windows installation!
>
> Reading the possible input files, I see that .psf files are not one of the
> acceptable files. Is there a reason why water molecules cannot be removed
> from psf files? For my particular case, I was interested in using catdcd to
> reduce the size of my dcd trajectories to be able to analyze them with the
> program MDContactCom, which requires dcd and psf files as inputs. However,
> if I remove the water molecules from the dcd file and not the psf file, I
> get this error:
>
> traj2pdb.py - Func: convert - ERROR - xyz must be shape (Any, 44191, 3).
> You supplied (200, 5508, 3)
>
> Searching online, this seems to be caused by a disconnect between the
> total number of atoms in the trajectory compared to the psf file (i.e. the
> lack of water in the dcd file). Is there a way to remove water molecules
> from the psf file?
>
> Thanks again for all the help.
>
> Best,
> Christos
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Friday, June 17, 2022 5:45 PM
> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
> *Cc:* Geist, Norman <norman.geist_at_uni-greifswald.de>; vmd-l_at_ks.uiuc.edu <
> vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: How to reduce the size of a .dcd file?
>
>
> ⚠ Caution: External sender
>
>
>
> On Fri, Jun 17, 2022 at 10:35 AM Efthymiou, Christos <
> christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> Additionally, is catdcd available on Windows? I cannot find any
> instructions or a manual on how to install and use the program.
>
>
> I have not installed VMD on Windows in a long time. It used to be that a
> catdcd executable is only included in some packages and not in the Windows
> package.
> Quite some time ago for some tutorials (and my own education), I had built
> Windows installer packages for catdcd. Those are still available at:
> https://urldefense.com/v3/__https://rpm.lammps.org/windows/testing/__;!!DZ3fjg!5kivWGm0CP5yG0P4vnCYnbPtYprlyU3i9C5PZXurWCYdX_j1A2V3E_rqS921FF8aoeHP3GDCp1BxKLZc6vPFbqsVPA$
> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Frpm.lammps.org*2Fwindows*2Ftesting*2F&data=05*7C01*7Cchristos.dereschuk.20*40ucl.ac.uk*7Cb9566f7fb1064fb4d79c08da5224b0cf*7C1faf88fea9984c5b93c9210a11d9a5c2*7C0*7C0*7C637912614792233125*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=pEQUjYh6CLNIH4bpqMp0qjR6LP4qOKcjWWOiNNXD0m4*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!_EZJ0-7dDkBwZuihvvAD14SQj1HUB4iT8OpltqKJgJt8J3uXsUxNiL188lfqG_zk0RKRA01756Cuf4dX7Ox5Wr7z4UV6mlg$>
> Use at your own risk. I just checked with a Windows 11 virtual machine and
> it can still be installed and run...
>
> Axel.
>
> ```
> Microsoft Windows [Version 10.0.22000.739]
> (c) Microsoft Corporation. All rights reserved.
>
> C:\Users\akohl>catdcd
> CatDCD 5.4
> catdcd -o outputfile [-otype <filetype>] [-i indexfile]
> [-stype <filetype>] [-s structurefile]
> [-first firstframe] [-last lastframe] [-stride stride]
> [-<filetype>] inputfile1 [-<filetype>] inputfile2 ...
>
>
> Allowed input file types:
> crd crdbox XDATCAR rst7 OUTCAR xml vcf vtf js car dcd namdbin POSCAR pqr
> cpmd dlpolyhist dlpoly3hist dlpolyconfig xyz tinker binpos ABINIT pdb
> lammpstrj hoomd cor bgf xsf gro g96 trr trj xtc pdbx xbgf cube mol2 dms dtr
> mae
>
> Allowed output file types:
> crd crdbox rst7 js dcd namdbin POSCAR pqr xyz binpos ABINIT pdb lammpstrj
> hoomd bgf gro trr pdbx xbgf mol2 dms dtr mae
> ```
>
> Thanks for the help!
>
> Best,
> Christos
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!5kivWGm0CP5yG0P4vnCYnbPtYprlyU3i9C5PZXurWCYdX_j1A2V3E_rqS921FF8aoeHP3GDCp1BxKLZc6vMQetDA9A$
> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=http*3A*2F*2Fgoo.gl*2F1wk0&data=05*7C01*7Cchristos.dereschuk.20*40ucl.ac.uk*7Cb9566f7fb1064fb4d79c08da5224b0cf*7C1faf88fea9984c5b93c9210a11d9a5c2*7C0*7C0*7C637912614792233125*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=XMa13zy07J*2BYhRq6RdkLczXAwRFPwm4dg5iRPCpb4LU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!_EZJ0-7dDkBwZuihvvAD14SQj1HUB4iT8OpltqKJgJt8J3uXsUxNiL188lfqG_zk0RKRA01756Cuf4dX7Ox5Wr7zMHLFjcg$>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>