[gmx-users] Thesis developed software; which Open-source License?

open-source licensing when distributing code? *Kind regards,* *Dr. Henry P.A. Wittler* *Department of Chemistry and Physics, LIMS, La Trobe University, MelbourneWorking in Ludvika, Sweden* *Skype: henry.wittler* Researchgate & Linkedin linkedin.com/in/henry-per-andreas-wittler-b032561

Re: [gmx-users] About g_sdf in version 4.6.5.

Darren, so generating SDF over several molecules is possible with the version you mentioned? Sincerely, Henry From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Tuesday, July 16, 2019 12:30:19 AM To: GROMACS users Subject

[gmx-users] About g_sdf in version 4.6.5.

still true with even newer versions, and also in 4.6.5? Sincerely Henry -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subs

[gmx-users] Visualising RDF selections

Dear GROMACS mailing list, Is there a possibility somehow to visualize (with VMD, for example) the point of center-of-mass which GROMACS appoints to a molecule when calculating Radial Distribution Functions (RDF) with option -rdf mol_com? Faithfully, Henry -- Gromacs Users mailing list

Re: [gmx-users] Details of g_rdf functions in version 4.6.5.

, RDF for atoms. But what atoms exactly? Faithfully, Henry From: Justin Lemkul Sent: Sunday 16 June, 02:41 Subject: Re: [gmx-users] Details of g_rdf functions in version 4.6.5. To: gmx-us...@gromacs.org On 6/14/19 1:15 AM, Henry Vider wrote: > Dear Warren, > > So if I understand you

Re: [gmx-users] Details of g_rdf functions in version 4.6.5.

7;s second atom, repeating it until the last Ethanol atom. Then selecting second atom of Ethyl Acetate and goes through the process again. And in the end the RDF is averaged over all these calculated interactions? Or is the formula of calculation some other ? Thank you Faithfully, Henry -O

[gmx-users] Details of g_rdf functions in version 4.6.5.

From: Henry Vider Sent: Thursday, June 13, 2019 11:37 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Details of g_rdf functions in version 4.6.5. Dear GROMACS mailing list, I am writing here due to the inconsistencies in my Radial Distribution Functions (RDF) calculations. Currently I

Re: [gmx-users] D- &/or L- cmap for charmm36

1.52 1.70 1.64 1.28 0.54 0.38 -0.07 Cheers, Henry On 10/4/16 2:00 AM, HENRY WITTLER wrote: > > Thanks, for the previous reply. > > Will the CHARMM cmap and topology for D-amino acids be included in gmx for a > later

Re: [gmx-users] D- &/or L- cmap for charmm36 (gromacs.org_gmx-users Digest, Vol 149, Issue 71)

this 'cgenff_charmm2gmx.py' at http://mackerell.umaryland.edu/charmm_ff.shtml#charmm Cheers, Henry Wittler Phd in Molecular modelling group (Brian J. Smith) Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Victoria 3086, Australia Tel: 0432901627

[gmx-users] D- &/or L- cmap for charmm36

looking at it in vmd etc, seems to imply that the .top, .itp do not distinguish about chirality, is this the case? How is cmap.itp implemented in gmx, is these parameters for L-, and D- aminoacids? Cheers, Henry Wittler Phd in Molecular modelling group (Brian J. Smith) Department of Chemistry

Re: [gmx-users] Beginner's problem: g_rdf functions and -com. Second attempt.

ticle and does operations with that? I hope you understood my explanation and I hope I did not go too in detail and drop the readers' interest. I hope anybody has time to answer this since it is quite important for my thesis. Thank you in advance, Yours

[gmx-users] Beginner's problem: g_rdf functions and -com

dy has time to answer this since it is quite important for my thesis. Thank you in advance, Yours faithfully, Henry V -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Randomly alter pdb start coordinates

tests started with one bash script, and one clean-up script resetting everything. Thanks, Henry Wittler Phd in Molecular modelling group (Brian J. Smith) Department of Chemistry, La Trobe University, Melbourne, Australia Tel: 0432901627 -- Gromacs Users mailing list * Please search the archive at