\001\001 Fatal error: Sorry, write_trxframe_indexed can not write cpt
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Correction -- in the first sentence:
... velocity coordinates (-ov) ...
Inon Sharony J+N+W+N% ShR+W+N+J+
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On 07/16/2012 02:19 PM, Inon Sharony wrote:
Good afternoon.
g_traj has the option to output position coordinates
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
: 1 (total 1 atoms)
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of the first time-step? This does
not happen when there is no coupling to the thermal bath.
Many thanks,
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Further information:
( conf.gro , topol.itp
found" 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 I would check whether this file outdated and change the error message accordingly if it is.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.
On 8/
website at http://www.gromacs.org/Documentation/Errors
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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 morning!
I'm running GMX
tau_T=0 for
some T-couple groups while using the sd integrator (just as is
accepted by the vv-avek integrator with the Nos-Hoover
thermostat)?
Thanks!
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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.
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] 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!
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of numbers in the function that prints to .trr .
Thanks in advance!
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Please
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 running a double-precision
installation of GROMACS, the printout to file (of the positions and
velocities) is of much less
,
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)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
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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!
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in advance,
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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 in advance,
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Lambda
10.000100.0
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MDRUN_MPI STD-I/O:
==
step 0
[hydrogen:15285] *** Process received signal
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
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]
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?
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Inon Sharony
.
Quoting Justin A. Lemkul jalem...@vt.edu:
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 Sharony wrote:
(Thanks, Justin)
I'm using GMX 4.0.4
in 2004:
http://www.gromacs.org/pipermail/gmx-users/2004-January/008600.html
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to get the
information I want?
Thanks,
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all of the (unnecessary) details?
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:
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?
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Please consider
?
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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,
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Handles: 0
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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
double-precision energy minimization for normal mode analysis
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:
so it's an improvement of more than 6
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 2:57 PM, Inon Sharony
[EMAIL PROTECTED] wrote:
I am preforming
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 point - I get only three significant digits.
Although I
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 energy minimization still does
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 order to be sure that
I'm
getting what
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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)
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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 precision, and it
came
out fine.
Could
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