On 1/17/13 9:54 AM, Marcelo Depolo wrote:
Well, Justin,
I tried to generate the .tpr using single precision and I got the same
warning. I also tried to use gmxcheck using the command line below:
*$ gmxcheck -e prt_cg.edr -m cg.tex*
Unfortunately, I got the same warning and no log file. What
On 1/16/13 12:36 PM, Marcelo Depolo wrote:
Justin,
I'm using gromacs 4.5.5 version, compiled in double precision. I tried to
generate the .tpr file 3 times and got the same results. About the
gmxcheck, i don't know how to use it to check my .edr file.
How can I do this?
Start with reading
Justin,
I'm using gromacs 4.5.5 version, compiled in double precision. I tried to
generate the .tpr file 3 times and got the same results. About the
gmxcheck, i don't know how to use it to check my .edr file.
How can I do this?
--
Marcelo Depólo Polêto
--
gmx-users mailing listgmx-users@grom
I have set nstenergy=100. I'm using gromacs compiled with double precision
and even so, the stepsize was too small.
i have faced this convergence problems earlier, and managed some solutions.
I'm really wondering about the warning part, that I have never seen.
--
Marcelo Depólo Polêto
--
gmx-user
On 1/16/13 12:11 PM, Marcelo Depolo wrote:
Thanks, Elton.
I appreciate your answer, but my question was about the Warning error. The
convergence value was set ok. The minimization do not go further because
the error:
*"WARNING: there may be something wrong with energy file prt_cg.edr
Found: s
On Wed, Jan 16, 2013 at 3:11 PM, Marcelo Depolo wrote:
> Thanks, Elton.
>
> I appreciate your answer, but my question was about the Warning error. The
> convergence value was set ok. The minimization do not go further because
> the error:
>
> *"WARNING: there may be something wrong with energy fil
Thanks, Elton.
I appreciate your answer, but my question was about the Warning error. The
convergence value was set ok. The minimization do not go further because
the error:
*"WARNING: there may be something wrong with energy file prt_cg.edr
Found: step=-1, nre=36, nblock=0, time=-1.
Trying to sk
On Wed, Jan 16, 2013 at 8:37 AM, Marcelo Depolo wrote:
>
> I was minimizing my system (with only proteins) and i got this error in the
> log:
>
> *Polak-Ribiere Conjugate Gradients:
>Tolerance (Fmax) = 1.0e-01
>Number of steps= -1
>F-max = 4.76837e+04
Thank you very much. It worked.
Regina
Quoting "Justin A. Lemkul" :
pol...@fh.huji.ac.il wrote:
Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't
sufficient". What information do you need in order be able to help?
I run EM wit
pol...@fh.huji.ac.il wrote:
Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't
sufficient". What information do you need in order be able to help?
I run EM with emtol=60 and I got the following energies:
Steepest Descents converge
Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't
sufficient". What information do you need in order be able to help?
I run EM with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
P
pol...@fh.huji.ac.il wrote:
Dear Gromacs users and developers,
I forgot to note that I'm talking about a Martini simulation.
I'm trying to set up simulation. I have a big simulation of something
like half million CG atoms. The problem is that I have a minimization
problem. I'm getting the fol
Dear Gromacs users and developers,
I'm trying to set up simulation. I have a big simulation of something
like half million atoms. The problem is that I have a minimization
problem. I'm getting the following error:
Converged to machine precision,
but not to the requested precision Fmax < 10
I
Dear Gromacs users and developers,
I forgot to note that I'm talking about a Martini simulation.
I'm trying to set up simulation. I have a big simulation of something
like half million CG atoms. The problem is that I have a minimization
problem. I'm getting the following error:
Converged to m
Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes,
Are you sure your error is not here? Inspect your result visually! :-)
All the atoms need to be inside the box and non-overlapping.
Mark
and now I want to perform a minimization
to remove the problems at their boundary! I have r
I think it is too small. Try removing the water molecule and repeat
the EM. You might need to remove some molecules before you can
minimise your system.
Itamar
On 26/10/2009, at 10:48 AM, Paymon Pirzadeh wrote:
Sorry,
That was a big typo(a mis-pasted line)!
What is the suggestion anywa
Sorry,
That was a big typo(a mis-pasted line)!
What is the suggestion anyway about emstep?
Payman
On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote:
> I am not sure what you refer to as dt, as there no meaning to time in
> EM.
>
> Anyway, I think the easiest way is to remove this war
I am not sure what you refer to as dt, as there no meaning to time in
EM.
Anyway, I think the easiest way is to remove this ware molecule.
Best,
Itamar.
On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote:
Hello,
I merged two simulation boxes, and now I want to perform a
minimization
to re
Hello,
I merged two simulation boxes, and now I want to perform a minimization
to remove the problems at their boundary! I have reduced the dt to
0.1 and emstep to 0.1 as well. But still I get the
message
Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision)
Maki
Hongyan Xiao wrote:
Hi,
I has used the periodic boundary conditions and correct em.mdp
file. However, the minimized result is water/decane/water, while I set
decane/water/decane as the initial system . I cannot understand the
reason. Please give me some constructive suggestion! Thanks!
You
Hongyan Xiao wrote:
Hi,
I has used the periodic boundary conditions and correct em.mdp
file. However, the minimized result is water/decane/water, while I set
decane/water/decane as the initial system . I cannot understand the
reason. Please give me some constructive suggestion! Thanks!
Hi,
I has used the periodic boundary conditions and correct em.mdp file.
However, the minimized result is water/decane/water, while I set
decane/water/decane as the initial system . I cannot understand the reason.
Please give me some constructive suggestion! Thanks!
H. Y. Xiao
_
Hongyan Xiao wrote:
Hi, David van der Spoel
I used the periodic boundary conditions. The box
is 3.006x3.002x6.000 along x,y,z direction,respectively.The following is
the em.mdp file.
Then the minimization works correctly. See chapter 3 in the manual.
;
; User xiao
; 2008.9.2
Hi, David van der Spoel
I used the periodic boundary conditions. The box is 3.006x3.002x6.000 along
x,y,z direction,respectively.The following is the em.mdp file.
;
; User xiao
; 2008.9.28 10:23
; Input file
;
cpp = /usr/bin/cpp
define = -DFLEXI
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