[gmx-users] First Circular: FOMMS 2009

The first circular for FOMMS 2009 is reproduced in this email below. Please forward to anyone who would be interested. Fourth International Conference Foundations of Molecular Modeling and Simulation FOMMS 2009 Foundations for Innovation Semiahmoo Resort, Blaine, WA, USA July 12 -16, 2009 http

[gmx-users] RSS feed for gromacs.org?

Is there an RSS feed for the "latest news" from gromacs.org? I discovered this link: http://www.gromacs.org/index2.php?option=com_rss&no_html=1 But it says you aren't authorized to view without logging in Jonathan Jonathan Moore, Ph.D. Research and Engineering Scien

[gmx-users] GROMACS 3.3.3 ?

Version 3.3.3 was expected to available "soon" back in November. What's the current estimate of its arrival date? Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 300E Midland, MI

RE: Re: [gmx-users] number of coordinates in coordinate file does not match topology

Christopher, I'm afraid I don't have any other ideas. To confirm if your editing method is OK, I would run a GROMACS example with an undmodified .mdp file and then modify it (making some trivial change) by your method and see if it still runs OK. Jonathan Jonat

RE: [gmx-users] number of coordinates in coordinate file does not match topology

Christopher, When I've had this problem before (# of coordinates in coordinate file does not match topology (0)), it has been because I edited the mdp file under Windows (mismatch between Windows and unix end-of-line characters). Is it possible that you have done the same? If so, try to run

RE: [gmx-users] number of coordinates in coordinate file does not match topology

Christopher, See this page for more info on this error: http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordi nate_file_does_not_match_topology Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemi

RE: [gmx-users] Implicit solvent simulation

I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN.

RE: [gmx-users] GROMACS Wiki

The email list, manual, etc. are good source material...but I think there will be added value in the wiki, even for answering specific questions. For example, for questions about complex topics like free energy, integration algorithms, parallel scaling, etc., it is rare that any single email me

RE: [gmx-users] about the topology file

Title: Message See the following from the archive for a possible source of the "number of coordinates...does not match" error.   http://www.gromacs.org/pipermail/gmx-users/2006-October/024223.html     Thanks, Jonathan Jonathan Moore, Ph.D. Research and Engineeri

RE: [gmx-users] RE: no coordinates in .top file

As I mentioned recently: http://www.gromacs.org/pipermail/gmx-users/2006-October/024137.html I get that kind of error ("number of coordinates in the coordinate file ( atoms) does not match topology (0 atoms)") when I've modified the .mdp file under Windows. Try opening the .mdp file under

RE: [gmx-users] grompp problems

I get that sort of error when I edit the .mdp file under Windows (mismatch between Windows and unix end-of-line characters). To avoid this, I try to never edit an mdp file in Windows. If I forget, it can be fixed by opening the file under unix and deleting all of the Windows end-of-line chara

RE: [gmx-users] g_traj -ng not working with option -ng

Title: Message By the way, another way to get the coordinates out is to use trjconv to read a .xtc (or whatever) and output a .gro (for example). Thanks, Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical

RE: [gmx-users] g_traj -ng not working with option -ng

Title: Message I submitted this as a bug a few days ago...   bug 107 http://bugzilla.gromacs.org/show_bug.cgi?id=107 Thanks, Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office

RE: [gmx-users] g_hbond

Behalf Of Erik Marklund Sent: Wednesday, August 23, 2006 7:28 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_hbond Ok. I'm on it. A few things I can see right away, other things need a closer look. See comments below On Tue, 2006-08-22 at 16:02 -0500, Moore, Jonathan (J) wro

[gmx-users] g_hbond

I'm still having problems with g_hbond. I've submitted a bugzilla report. - The hbond existence matrix in the -hbm output does not match the list of hbonds in the ndx file from -hbn. - Also, it outputs "No option -g" when no -g command line option has been tried - Also, sometimes the number of

[gmx-users] compiling an old gmx version under cygwin

I recently installed a hacked version of gmx 3.0 under cygwin (yes, I know 3.0 is ancient, but I'm using it in this case because of some extra functionality that this hacked version has). configure informed me "cannot find -lnsl" and "WARNING: RPC/XDR libraries not found - disabling xtc". I didn

RE: [gmx-users] re: need help with free energy of solvation calcu lation

David M., Thanks for the suggestions. About the Yu et al. error bars: > For Yu et > al., the first number is the average from the full 5 ns simulation and > the number in () is for the last 2 ns. If not for the CE23Me case, I would probably assume that the discrepancy due to doing a notorio

[gmx-users] re: need help with free energy of solvation calculation

This is a follow-up from my post in January regarding my attempts to reproduce some free energy of solvation calculations for modified cellulose oligomers. First, a question: I know that certain values of sc-alpha are preferred for different cases, but are there any values that definitely shoul

[gmx-users] email list archives problem on new web site

FYI - on the new web site, the links to the archives of all of the email lists go to the gmx-announce archives. Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 4E Midland, MI 486

RE: [gmx-users] g_hbond question

sday, March 23, 2006 12:27 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_hbond question try g_hbond -g! daniela On Wed, 2006-03-22 at 06:15 -0600, Moore, Jonathan (J) wrote: > Daniela, > > Thanks for that tip. It looks like that won't help me, though, >

RE: [gmx-users] g_hbond question

ject: Re: [gmx-users] g_hbond question hi jonathan, the actually occuring hydrogen bonds are listed in the log-file. daniela On Tue, 2006-03-21 at 14:56 -0800, Moore, Jonathan (J) wrote: > I created a hydrogen bond map using g_hbond of version 3.3. The > manual indicates that for the hb

[gmx-users] g_hbond question

I created a hydrogen bond map using g_hbond of version 3.3. The manual indicates that for the hbmap the "Ordering is identical to that in -hbn index file." However, in my case, the hbmap file contains 13 hydrogen bond indices, but the hbond.ndx file lists 20 sets of donors and acceptors. Why

RE: [gmx-users] output frequency to dgdl.xvg

9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess Sent: Friday, March 17, 2006 12:02 PM To: gmx-users@gromacs.org Subject: RE: [gmx-users] output frequency to dgdl.xvg >From: "M

[gmx-users] output frequency to dgdl.xvg

Is there a way to control the frequency of output to dgdl.xvg? Writing a value every timestep is overkill and can waste significant disk space if you're simulating many lambda points and many systems. Thanks, Jonathan Jonathan Moore, Ph.D. Research and Engineering S