[gmx-users] RE: נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

I thought setting tau_t=0 for some of the groups means that they're not coupled. That is tau_t would in fact be infinite, but that would be more difficult to input, whereas if tau_t were actually equal to zero the situation (as you described it) would lack physical significance... Since only the No

[gmx-users] Re: Positions and velocities from trajectory for restart

Correction -- in the first sentence: "... velocity coordinates (-ov) ..." Inon Sharony J+N+W+N% ShR+W+N+J+ [1]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 On 07/16/2012 02:19 PM, Inon Sharony wrote: Good afternoon. g_traj has the option to output position c

[gmx-users] Positions and velocities from trajectory for restart

uot;Source code file: trxio.c, line: 269 \001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt" -- Inon Sharony J+N+W+N% ShR+W+N+J+ [1]http://atto.TAU.ac.IL/~InonShar +972-3-640-7634 References Visible links 1. http://atto.tau.ac.il/~InonShar -- gmx-users ma

[gmx-users] נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

tcoupl =v-rescale  See grompp .mdp  below  Inon Sharony ינון שרוני "Berk Hess [via GROMACS]" כתב: Hi, You can't have ret_t=0 with Nose-Hoover. We should add a check for this. Cheers, Berk > Date: Thu, 28 Jun 2012 11:15:15 +0300 > From: [hidden email] > To: [

[gmx-users] Nose-Hoover does not couple

Acceleration: 1 (total 1 atoms) Freeze : 1 (total 1 atoms) User1 : 1 (total 1 atoms) User2 : 1 (total 1 atoms) VCM : 1 (total 1 atoms) XTC : 1 (total 1 atoms) Or. Res. Fit: 1 (total 1 atoms)

[gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain

ities after the beginning of the first time-step? This does not happen when there is no coupling to the thermal bath. Many thanks, -- Inon Sharony J+N+W+N% ShR+W+N+J+ 972-3-6407634 Please consider your environmental responsibility before printing this e-mail. Further information:

[gmx-users] Re: md.log i/o error in futil.c +459

d" as opposed to "md.log could not be opened" instead of "file i/o error"). Also, I still don't understand under which directory futil.c is located. I would check whether this file outdated and change the error message accordingly if it is. Thanks for your time, Inon.

[gmx-users] md.log i/o error in futil.c +459

ocumentation/Errors --- "Everything Must Go" (Red Hot Chili Peppers) -- Inon Sharony ינון שרוני 972-3-6407634 Please consider your environmental responsibility before printing this e-mail. -- gmx-users mailing

Re: [gmx-users] Temperature de-coupling in Langevin Dynamics

Good morning, Mark! How do I officially request this as a feature of the next version of GROMACS? Post to the developers' forum? Thanks, Inon. On Saturday, December 24, 2011 12:24:11 PM UTC+2, Mark Abraham wrote: > > On 12/24/2011 6:23 PM, Inon Sharony wrote: > > Good

[gmx-users] Temperature de-coupling in Langevin Dynamics

e be altered to accept tau_T=0 for some T-couple groups while using the sd integrator (just as is accepted by the vv-avek integrator with the Nosé-Hoover thermostat)? Thanks! -- Inon Sharony ינון שרוני 972-3-6407634 Please consider your environmental responsibility befor

[gmx-users] revive gmx-announce

rm it as an RSS or atom feed) so that the really important announcements that come out only once-in-a-while could be disseminated without the need to get every post from the users' list. Thanks for your time, -- Inon Sharony ינון שרוני 972-3-6407634 Please consider your environmental resp

[gmx-users] mdatoms->massA pointer dereferencing

m gets value zero ) and as soon as "md->massA[trajectory_atom]" is accessed, the program crashes. This was the result I got before. I tried accessing only elements 1 and above (by changing trajectory_atom to trajectory_atom+1 ) but got the same result. Thanks! -- Inon Sharon

Re: [gmx-users] Precision in trajectory file

uble-precision > GMX, the leap-frog integrator is using double-precision coordinates, but > the printed value in .trr is also truncated due to the format problem. > > > > Inon Sharony wrote: > > Good afternoon! > > > > It seems to me that although I'm ru

[gmx-users] Precision in trajectory file

of changing the format of numbers in the function that prints to .trr . Thanks in advance! -- Inon Sharony ינון שרוני 972-3-6407634 Please consider your environmental responsibility before printing this e-mail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] Re: Re: help with gmx C source code

nks for all the help, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] Re: help with gmx C source code

ugging symbols found) (no debugging symbols found) [Thread debugging using libthread_db enabled] (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (no debugging symbols found) (

[gmx-users] help with gmx C source code

w one becomes a GROMACS source contributor or developer, but so far I've been having a tough time getting help with the (open) source code. Any and all help would be greatly appreciated! -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environme

[gmx-users] printing to edr in source code

? Thanks in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] SD temperature coupling groups

0] = 1, the simulation ran properly. Where in the code can I check that what is written in the manual is, indeed correct? (i.e., I expect an if statement saying that if the tau-T value of some temperature coupling group is zero, then take the inverse of that to be effectively zero). Thanks i

[gmx-users] segfault(11) -- simulation blows up on first step

Sorry for the previous mail, I guess the appended content was too long. Anyway, here it is as an attached file Sorry, and thanks again -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail

[gmx-users] segfault(11) -- simulation blows up on first step

nan Step Time Lambda 1 0.000100.0 -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. MDRUN_MPI STD-I/O: == step 0

[gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching

home people). Inon. Quoting "Justin A. Lemkul" : > > Your problem is unrelated to the bug. Something in your system is > crashing; this is a commonly-reported problem (search the archives). > > Your system only contains three atoms? > > -Justin > > Inon Sha

[gmx-users] Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching

] In response to the suggestion within the message, my tiny three-atom molecule is optimized to a force of 1E-9. I also turned off Dynamic Load Balancing, in the hope that this might help, but alas... Any thoughts on what I might be doing wrong, and how I could check for it/them? -- Inon Sh

[gmx-users] Has anyone adapted an Allinger force field for GROMACS? (MM,MM+,MM2,MM3...)

2004: http://www.gromacs.org/pipermail/gmx-users/2004-January/008600.html Thanks in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail.___ gmx

[gmx-users] pair forces

n idea how to get the information I want? Thanks, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ gmx-users mailing listgmx-users@gromac

[gmx-users] override dispalying of options

to call these functions without having to display all of the (unnecessary) details? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ gmx-users

[gmx-users] empty velocity *.xvg file from g_traj

gives me two *.xvg files: the x_ndxgrp1 file is fine, but v_ndxgrp1 has an xmgrace formatting header, and then no data afterward. This formatting information agrees with the number of atoms in the group ndxgrp1. what am I doing wrong? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.a

[gmx-users] splitting a trajectory according to atoms using trjconv

groups or atoms? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. Links: -- [1] http://bugzilla.gromacs.org/show_bug.cgi?id=107) ___ gmx-users mail

[gmx-users] manipulation of trajectory data

s many comments, but I find it hard to understand. If anyone has a simpler example along the lines of my interests, please send me it! Thanks very much in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before

Re: [gmx-users] single-precision *.tpr data after a double-precision run

r file, so I'll just include the *.trr every time I run NMA. The em step is not specified in the nm.mdp file, so I guess I could add it (and specify 1E-05) and I hope that will help. Thanks again. Inon. Quoting "Ran Friedman" <[EMAIL PROTECTED]>: Inon Sharony wrote: s

Re: [gmx-users] single-precision *.tpr data after a double-precision run

quot; <[EMAIL PROTECTED]>: Hi, I'm not sure if this is the problem but did you try to include the energy and trajectory files when running grompp (flags -e and -t)? Ran. Inon Sharony wrote: Hello GROMACS users! I've posted a few questions in the last few days about doubl

[gmx-users] single-precision *.tpr data after a double-precision run

e these last two decimal places anew, and this makes the difference in SEVEN orders of magnitude in the maximal force? Can anyone offer a solution? Thanks in advance... Inon. Some background information: I'm running GROMACS 3.3.3 on the following system (w

Re: [gmx-users] Normal Mode Analysis in Double-Precision

macs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mai

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Quoting "Ran Friedman" <[EMAIL PROTECTED]>: Inon Sharony wrote: Dear Ran, I'm still unsure of why I sometimes can get double-precision output and sometimes not. I can't find what I'm doing differently in each case, however I now know what to look for in orde

Re: [gmx-users] Normal Mode Analysis in Double-Precision

program (didn't know at the time that I can "make" only one function). Now the g_anaeig_d works fine (as best as I can tell). Thank you so much for all of your help! Inon. Quoting "Ran Friedman" <[EMAIL PROTECTED]>: Inon Sharony wrote: This is exactly the poin

Re: [gmx-users] Normal Mode Analysis in Double-Precision

veral cycles of EM, say CG and then L-BFGS to get better convergence. Ran. Inon Sharony wrote: I now performed: make distclean ./configure --disable-float make make install make links All executed without problems. Now I no longer have segmentation faults (thanks David!), however the ener

Re: [gmx-users] segmentation fault in g_anaeig

ably) most important piece of information: what version are you using? (You might also want to include platform, OS, compiler, etc.). Note that just a few days ago it was already reported on this list that g_anaeig of version 3.3.3 gave a segfault. Cheers, Tsjerk On Sun, Aug 3, 2008 at 2

[gmx-users] segmentation fault in g_anaeig

nificant digits to the right of the decimal point are non-zero). Any and all assistance would be greatly appreciated. Enjoy your weekend, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before print

Re: [gmx-users] Normal Mode Analysis in Double-Precision

search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Inon Sharony ינון שרונ×

Re: [gmx-users] Normal Mode Analysis in Double-Precision

t minimize below a maximal force of about 1e-3 kJ / mole nm .) What does this mean? Thanks Inon. Quoting "Ran Friedman" <[EMAIL PROTECTED]>: Inon Sharony wrote: Hi Ran. I looked up your suggestions, and got the following: 0. The parameters in the *.tpr file appear in

Re: [gmx-users] Normal Mode Analysis in Double-Precision

les for me to compare with? Assuming you've run Normal Mode analyses in the past... Thanks very much again, Inon. Quoting "Ran Friedman" <[EMAIL PROTECTED]>: Inon Sharony wrote: Hi Ran, thanks for the reply I ran "make tests" after compiling with double

[gmx-users] Normal Mode Analysis in Double-Precision

le precision. It was suggested that I insert a "print to screen" line in the source code immediately after the *.gro file is read, to see if the printed data is in single-precision or double-precision format. What do you think? Thanks again, everyone -- Inon Sharony ינון

[gmx-users] Normal Mode Analysis in Double-Precision

meone with experience in Normal Mode analysis in GROMACS (or just general experience in using GROMACS with double-precision) help me with my difficulty? (Currently I'm running pentane or para-dimethylbenzene) Thanks for your help, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.