Dear Mark,
I found a simple(est) fix to this problem. Say in my case I was getting
error inf on atom 4281 ( Maximum force =inf on atom 4281)
What I did: In gro file for atom number 4281 I edited one of its
coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x,
That procedure can work. That it works in your case surprises me a little.
:-)
Mark
On Thu, May 2, 2013 at 11:25 AM, gromacs query gromacsqu...@gmail.comwrote:
Dear Mark,
I found a simple(est) fix to this problem. Say in my case I was getting
error inf on atom 4281 ( Maximum force =
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy = 4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =inf
(inf means? means infinite/NAN)
I removed the full lipid residue having
On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy = 4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =
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.
On Wed, Jan 16, 2013 at 8:37 AM, Marcelo Depolo marcelodep...@gmail.com 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
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
On Wed, Jan 16, 2013 at 3:11 PM, Marcelo Depolo marcelodep...@gmail.com 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
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:
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
--
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 list
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
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax 10
Double precision normally
On 7/26/12 8:30 AM, tarak karmakar wrote:
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested
Dear Gmx Users,
I would like to run energy minimization with some atoms restrained - this
is a surface made of atoms which do not share any bonds. So the EM of water
only. I tries to use define = -DPOSRES
in my EM file but then the surface atoms change their positions. Thus, when
I want to run
On 5/16/12 5:54 AM, Steven Neumann wrote:
Dear Gmx Users,
I would like to run energy minimization with some atoms restrained - this is a
surface made of atoms which do not share any bonds. So the EM of water only. I
tries to use define = -DPOSRES
in my EM file but then the surface atoms
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
for a few interactions, with each of them approaching inf.
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase
On 2/02/2012 3:36 PM, Alex Seling wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
for a few
On 2/02/2012 3:42 PM, lina wrote:
On Thu, Feb 2, 2012 at 12:36 PM, Alex Selingselin...@msu.edu wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't get
any error while performing the minimization but when visualised the pdb file
after the minimization the chains of the protein complex separated.
What could be the reason.
Thanks,
Aiswarya
Sent from my
1 check with the rtp files in your forcefield, especially the parameters
2 check with the imput pdb file, the format matters a lot.
On Wed, Oct 19, 2011 at 8:18 AM, aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any
aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't get
any error while performing the minimization but when visualised the pdb file
after the minimization the chains of the protein complex separated.
What could be the reason.
Hi,
All the parameters are ok, still i get the complex separated.
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any error while performing
On 20/10/2011 4:14 PM, aiswarya pawar wrote:
Hi,
All the parameters are ok, still i get the complex separated.
Simulation parameters have nothing to do with the phenomena in the FAQ
Justin pointed out to you. Please read it.
Mark
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul
Thank you very much. It worked.
Regina
Quoting Justin A. Lemkul jalem...@vt.edu:
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?
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
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
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
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 converged
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the same
post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field.
my box dimensions are 368A
Quoting chris.ne...@utoronto.ca:
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the
same post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run
Quoting pol...@fh.huji.ac.il:
Dear gromacs users,
my box dimensions are 368A and when I run the simulation with
nsteps=1 it works fine. The mdp files used for minimization and
post-em simulation are attached.
Thanks again for your help.
Regina
Quoting chris.ne...@utoronto.ca:
What are
Can you please redo the md part with gen_vel=yes and see if that makes
any difference?
Generally, you need to narrow down the problem for us. Does it crash in
serial as well as parallel? How many steps does it go before the crash?
what happens to the system volume as a function of time for
Hello,
I have an input structure with poor torsion angles and after minimization with
gromacs (both steepest descent and congugate gradient) I found that they were
not corrected. There is enough free space for the torsion angles to be
corrected.
(I am sure of this because when I run the
On 8/02/2011 2:47 AM, abdullah ahmed wrote:
Hello,
I have an input structure with poor torsion angles and after
minimization with gromacs (both steepest descent and congugate
gradient) I found that they were not corrected. There is enough free
space for the torsion angles to be corrected.
(I
Dear Gromacs users,
I wanted to know whether it is correct doing minimization
in double precision and rest all - pdb2gmx, editconf, genbox,
grompp and mdrun itself in single precision.
I had got convergence during energy minimization using double
precision but not single precision (input
Hi all,
At the end of the minimisation I obtained potential energy value
approximately -40,000 and I see the following warning
Stepsize too small, or no change in energy.Converged to machine precision,
but not to the requested precision Fmax 10
As far as I know for succesful minimisation
mustafa bilsel wrote:
Hi all,
At the end of the minimisation I obtained potential energy value
approximately -40,000 and I see the following warning
Stepsize too small, or no change in energy.Converged to machine
precision, but not to the requested precision Fmax 10
Please see the
Dear Justin,
I have added your last reply to the end of this message.
my shell type is bash.
my dssp exe file is in /home/m/DSSP/dssp
I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did
do_dssp I have the below error. Although the dssp exe is in /usr/local/bin
and also I did
Hi,
What is the meaning of the below message after I completed minimization?
Does it mean minimization is successful?
In my input parameters nsteps=10,000,000 but minimization stops at about
14,000 th step. Is 10,000,000 very large? What is the typical value for it?
And also what is the meaning
mustafa bilsel wrote:
Dear Justin,
I have added your last reply to the end of this message.
my shell type is bash.
my dssp exe file is in /home/m/DSSP/dssp
I wrote export DSSP=//home/m/DSSP/ as in gromacs web page, then I did
This is still wrong. As I quoted in the previous message, the
mustafa bilsel wrote:
Hi,
What is the meaning of the below message after I completed minimization?
Does it mean minimization is successful?
In my input parameters nsteps=10,000,000 but minimization stops at about
14,000 th step. Is 10,000,000 very large? What is the typical value for it?
Hello everyone,
I have a question regarding the results of minimization. I have two structures
that are the same except for 2 residues in the core of the structure that have
been changed from luecine to to glycine. The leucine structure is very well
packed and the core is hydrophobic. The
- Original Message -
From: abdullah ahmed abdullah_renk_ah...@hotmail.com
Date: Wednesday, September 15, 2010 21:18
Subject: [gmx-users] minimization quagmire
To: gmx gmx-users@gromacs.org
!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size:
10pt; font
Dear Gromacs Users,
I am unable to minimize a complex protein (Trimer-Trimer complex) to even less
than Fmax=1.754e+00.
I tried few tricks like performing MD for few steps etc, but it does not yield
any results.
I am sure there must be a way out. Can you please advice.
Thanks for your
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)
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
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 ware
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
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
Hi Morteza,
How did you obtain these structures? If they were modeled, maybe in
part, check for knots and chain overlaps. Also check whether you're
using PBC and if so, whether the box is large enough or you may have
overlapping periodic images.
Cheers,
Tsjerk
2009/8/13 Mark Abraham
Dear Tsjerk
Thanks for your suggestion...actually It is a crystal structure...the
problem happen when I want to minimize the structure in vacuumthe box
size is enough...but the problem is that the minimization is fine with
gromacs forcefield but it is not ok with OPLSAA forcefiledI tried
Morteza Khabiri wrote:
Dear Tsjerk
Thanks for your suggestion...actually It is a crystal structure...the
problem happen when I want to minimize the structure in vacuumthe box
size is enough...but the problem is that the minimization is fine with
gromacs forcefield but it is not ok with
Hmm, was the OPLSAA run following the GMX one on the dimer or also
performed on the monomers? If you feed a multimeric protein without
chain identifiers (like in a .gro file) to pdb2gmx, it will bind the
different chains together. That would be a good cause for a crash. So
I'd say check that
:03 +0200 (CEST)
From: Morteza Khabiri khab...@greentech.cz
Subject: [gmx-users] minimization
To: gmx-users@gromacs.org
Message-ID:
25565.160.217.215.124.1250155803.squir...@www.greentech.cz
Content-Type: text/plain;charset=iso-8859-2
Dear Tsjerk
Thanks for your suggestion...actually
Dear MARK and Tsjerk
I found somethingafter making topology file by pdb2gmx ... I made tpr
file by grompp ... then I give the original pdb file and tpr file to ngmx
to see the system before running minimization...the interesting thing was
that the bonds between atoms are stretched..
I
Hi Morteza,
I think it will be best for all of us if you can provide the exact
command lines you are using, and the output of pdb2gmx for the
well-performing and an ill-performing force field. Otherwise I'm
afraid that we will not be able to get any further than making
guesses.
Cheers,
Tsjerk
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step, change coulomb type ,... but
Morteza Khabiri wrote:
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step,
On 08/07/09, Morteza Khabiri khab...@greentech.cz wrote:
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step, change coulomb type ,... but
Morteza Khabiri wrote:
Dear users
I have a dimer protein which I want to minimized it..unfortunately the
protein is in high energy level and before starting to minimize it
explode.
I already went through users email and also wiki gromacs and also I tried
all the way like changing time step,
Dear users
I want to minimized a dimer protein but at the first step it start to
explosion. I tried to decrease the dt but it is not working. the protein
is in the high energy level. Is there any suggestion how to minimized such
a high energy level protein??
thanks
Morteza Khabiri wrote:
Dear users
I want to minimized a dimer protein but at the first step it start to
explosion. I tried to decrease the dt but it is not working. the protein
is in the high energy level. Is there any suggestion how to minimized such
a high energy level protein??
There are
Hi,
I think that my minimization are not running long enough. I've been
following the parameters in tutorials but it seems like they all die
at 34 steps
I've been using these tutorials
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
Hongyan Xiao wrote:
Hi, gmx-users,
I built a system,decane(42molecule)/water(903)/decane(42), including the
two decane/water interfaces. However, when I minimized this system, I
found the system turn into water/decane(84)/water. That is to say in
the initial system two parts of decane turn
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
;
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,
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!
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!
Date: Thu, 27 Mar 2008 12:59:06 -0700
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
Berk,
I assume you are using a rigid water model, and thus constraints via SETTLE.
Yes, OK.
Constraining is required
David Mobley wrote:
Xavier,
I was surprised by the value you use for emstep=1.0e-8. This is the
maximum step size and is in nm! I think that's where your problem is.
I added this recently in testing because I thought perhaps the problem
could be due to using too large of steps. It does not
Date: Thu, 27 Mar 2008 07:54:03 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
David Mobley wrote:
Xavier,
I was surprised by the value you use for emstep=1.0e-8. This is the
maximum step size
Hello
I'm trying to minimize a protein with the a part of it frozen.
I was wondering if it is at all possible to extract bonded energy
terms for the non-frozen region.
I can extract the coulombic and LJ energy terms but not the bond,
angle and proper dih ones...
Any suggestions?
Thanks a
Berk,
The problem could be in the constraints.
Gromacs 3 constrains the forces during EM by adding c*f to the coordinates,
constraining those and then dividing the constraint displacement by c.
This limits the accuracy.
In Gromacs 4 I have implemented force constraining for LINCS and
Date: Thu, 27 Mar 2008 06:41:12 -0700
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
Berk,
The problem could be in the constraints.
Gromacs 3 constrains the forces during EM by adding c*f to the coordinates
Berk,
I assume you are using a rigid water model, and thus constraints via SETTLE.
Yes, OK.
Constraining is required to measure the size of the force (for convergence
and
step size adjustment) and to make correct steps without enormous extra
displacements in the direction of the force
Berk,
Hmm. Is this different from how other packages handle this issue? I
have never had the recurring problems with minimization in GROMACS
that I have in other packages. Even though, strangely enough, water is
a common feature in most of the simulations I run.
That was backwards. I
All,
I often have problems with minimization in gromacs, but now I think I
have something a little more systematic to say.
First, my system: I am simulating a short peptide in a mix of two
co-solvents. I use a program called packmol which can start pack
specified number of molecules into a box
Hi David,
I was surprised by the value you use for emstep=1.0e-8. This is the
maximum step size and is in nm! I think that's where your problem is.
The minimizer is probably incapable to find anything better for your
system with this step size and therefore stops.
Did you try to keep the
Xavier,
I was surprised by the value you use for emstep=1.0e-8. This is the
maximum step size and is in nm! I think that's where your problem is.
I added this recently in testing because I thought perhaps the problem
could be due to using too large of steps. It does not help. So
everything I
David Mobley wrote:
Also, I think your argument is backwards: steepest descents should
work better (but slower) the smaller the step size, I think. If steps
are too big it won't be able to move down the gradients accurately
enough and risks not being able to find the minimum. The smaller the
Mark,
However should you find yourself on a very flat area of the PES, then
the smaller the step size, the closer it will look to flat, and thus to
have converged to a stationary point. Flat is of course relative to
the step size
Right. But of course the problem here has is that the
David Mobley schrieb:
Hi David,
enough and risks not being able to find the minimum. The smaller the
steps are the more accurately it should be able to find the minimum.
mmh, just my 0.02€: I guess in a very rough energy landscape (as in
solvated peptides or proteins) this is not generally
Dear Christian,
mmh, just my 0.02€: I guess in a very rough energy landscape (as in
solvated peptides or proteins) this is not generally true, because
with small steps the system might get stuck in the next tiny local
minimum, while with a larger step size it may jump across it.
And I
Hi all,
As you suggest David I used genconf command without -rot option. I minimized a
single capped trp molecule and got the minimized molecule and used that
molecule with genconf command in order to create a box.
Then, I solvated capped trp molecule within the created box with genbox
OZGE ENGIN wrote:
Hi all,
As you suggest David I used genconf command without -rot option. I minimized a single capped trp molecule and got the minimized molecule and used that molecule with genconf command in order to create a box.
Then, I solvated capped trp molecule within the created box
Hi,
I'm getting a quirky result from my minimization of my system (which
consists of a small peptide in a membrane, solvated).
When I look at the trr of the minimization (or the outputted structure
after minization), I notice that my membrane has been inverted, and
there are 4 copies
Hi Arneh,
I guess it's the PBC. Did you center your bilayer at z=0 (or x, or y)?
Then it's certain it's the PBC. Next time it may be better to center
your system at the box center.
Best,
Tsjerk
On 9/21/06, Arneh Babakhani [EMAIL PROTECTED] wrote:
Hi,
I'm getting a quirky result from my
Ahh! Yes, Indeed I did center it to 0 0 0. I corrected that (centered
it in the box), and it works fine now.
Thanks Tsjerk,
Regards,
Arneh
Tsjerk Wassenaar wrote:
Hi Arneh,
I guess it's the PBC. Did you center your bilayer at z=0 (or x, or y)?
Then it's certain it's the PBC. Next time it
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