[EMAIL PROTECTED] wrote:
Hello,
I am trying to track down the exact nature of the gcc-4.1.x / gromacs
bug. I have a system on which we were forced to reinstall gromacs (3.3.1
and 3.3.3) about 2 weeks ago and I didn't realize that the default gcc
was bumped to 4.1.2.
I am interested because
Hello GROMACS users!
I've posted a few questions in the last few days about
double-precision energy minimization for normal mode analysis, and
everything seems OK except I've been having a re-occurring problem:
The energy minimization procedure ends in
Dear GMX users,
I've uploaded a version of g_covar that can be used to calculate the
correlation of motion between atoms to the user contributions. I hope
some of you would find it useful.
Ran
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Hi Justin,
In addition to that, you may consider using pbc = full to get an
infinite system and potentially avoid some of those edge effects it
looks like you are seeing. I know others have used that kind of
setup with carbon nanotubes (not my area of expertise, but I've read
the
Hi Andre,
if you are not interested in the substrate dynamics, then you could
try the freeze group options (freezegrps and freezedim). I have used
these options for graphite and it worked just fine.
Thanks for your reply! In addition with the 'pbc = full' options it solves all
my problems
Amazing! It didn't say anything about double-precision, and I got:
Maximum force: 4.32762e-04
(this is from the Hessian calculation, after minimization that got
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax 1e-06
writing
Michael Hirtz wrote:
Hi Justin,
In addition to that, you may consider using pbc = full to get an
infinite system and potentially avoid some of those edge effects it
looks like you are seeing. I know others have used that kind of
setup with carbon nanotubes (not my area of expertise, but I've
Dear All,
I have a problem when I use ACE patch in one of my proteins using FFG43a1.
I am issuing:
pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro
I am using -ter because I already have ACE at N terminus and NH2 at C-terminus.
I used this test.gro and put it in a water box and went ahead with
Inon Sharony wrote:
so it's an improvement of more than 6 orders of magnitude! Could it be
that the *.trr file have the coordinates in double-precision?
Right.
Not to be petty, but still, I had a max. force of 5.38105464411935e-05
using the minimization procedure, and the Hessian calculation
I checked the *.trr, it does in fact show the coordinates in
double-precision (as opposed to the output *.tpr file). I don't know
why this is, but as long as I get a decent enough max. fore (i.e.
~1E-05) I'll just leave it at that. I didn't see anything relevant in
the *.edr file, so I'll
Inon Sharony wrote:
I checked the *.trr, it does in fact show the coordinates in
double-precision (as opposed to the output *.tpr file). I don't know
why this is, but as long as I get a decent enough max. fore (i.e.
~1E-05) I'll just leave it at that. I didn't see anything relevant in
the
This means that although the minimization was run in double precision,
the atomic configuration is saved in single precision (the last two
decimal places are not used). Does this mean that each time the
optimized *.gro file is re-read, it needs to optimize these last two
decimal
That sounds good, but I'm not sure if it is enough.
Agreed. I'll recompile and start from previous checkpoints.
Did you select Closed bugs as well?
ouch! You're right, thanks for the tip.
The error is mentioned here:
http://bugzilla.gromacs.org/show_bug.cgi?id=108
and
M. Emal Alekozai wrote:
Dear All,
I have in a mdrun.mdp file following settings:
; mode for center of mass motion removal =
comm-mode= Linear
; number of steps for center of mass motion removal =
nstcomm = 1
; group(s) for center of mass
Romelia Salomon wrote:
Hi
I am trying to set a calculation based on the GROMOS force field in a
program I have and I am using GROMACS to generate the (starting) input
files for me. From reading the manual I know that GROMOS uses a fourth
power potential (type 2) for bonds and a cosine based
I would like to use air as a solvent with genbox instead of water. I have
read the manual but have not found any information to help me. Any
information would be beneficial.
Thanks,
Andy
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gmx-users mailing listgmx-users@gromacs.org
Andy Shelley wrote:
I would like to use air as a solvent with genbox instead of water. I
have read the manual but have not found any information to help me. Any
information would be beneficial.
There is no real automated way to make your own exotic solvents. If you have
coordinate files
Hi,
2. If the option comm-grps = Protein SOL physical means (1b) what do
I have to change in my simulation setup to avoid the warnings/ error
T-cm: inf in the log files?
comm-grps = System (as you noted, it does not give the error!)
I forgot to mention that my system contains except the
Hi Justin
thanks for your email, yes I used the -pp option to print out the file I
showed here. I am using gromacs-3.3.3 and I compiled it just doing the
typical ./configure make make install and I checked and it's using cc as a
compiler.
What I was trying to do is to run a calculation using
Quoting M. Emal Alekozai [EMAIL PROTECTED]:
Hi,
2. If the option comm-grps = Protein SOL physical means (1b) what do
I have to change in my simulation setup to avoid the warnings/ error
T-cm: inf in the log files?
comm-grps = System (as you noted, it does not give the error!)
I
Quoting Justin A. Lemkul [EMAIL PROTECTED]:
Quoting Romelia Salomon [EMAIL PROTECTED]:
Hi Justin
thanks for your email, yes I used the -pp option to print out the file I
showed here. I am using gromacs-3.3.3 and I compiled it just doing the
typical ./configure make make install and I
Ok, for my ligand I was using the Dundee PRODRG Server and the file
produced reads like this for example:
[ bonds ]
; ai aj fuc0, c1, ...
1 2 10.153334720.00.153334720.0 ; CAB CAE
2 3 10.139418400.00.139418400.0 ; CAE CAD
3 4 1
Romelia Salomon wrote:
Ok, for my ligand I was using the Dundee PRODRG Server and the file
produced reads like this for example:
[ bonds ]
; ai aj fuc0, c1, ...
1 2 10.153334720.00.153334720.0 ; CAB CAE
2 3 10.139418400.00.139418400.0 ;
Oh!! thanks!!... gromos, gromacs... that little x escaped my attention :)
That should solve all my doubts, thanks a lot!!
Romelia
Romelia Salomon wrote:
Ok, for my ligand I was using the Dundee PRODRG Server and the file
produced reads like this for example:
[ bonds ]
; ai aj fu
I am trying to do a simulation of prtein molecule having 460
residues(including hetero atoms).it works well till genbox,but while running
grompp its giving following error..
1-4 interaction between 97 and 104 at distance 1.558 which is larger than
the 1-4 table size 1.000 nm
I am not getting
priyanka srivastava wrote:
Dear All,
I have a problem when I use ACE patch in one of my proteins using FFG43a1.
I am issuing:
pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro
I am using -ter because I already have ACE at N terminus and NH2 at
C-terminus.
I used this test.gro and put it in a
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