Re: [gmx-users] The energy minimization....

[MoJie Duan]

Hi, Mark:I have done the energy minimization and simulation of ATP in vacuum individual ( Maybe you have suggested me to do this yesterday, but actually I did not understand it, and just do this in solution).There are following problems:1. in the energy minimization, the potential energy is positive and in 14th step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just the same as the original file (i.e. the .gro file before minimization), the return messages of mdrun is (there are not any warning):--Getting Loaded...Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)Loaded with MoneyBack Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#Steepest Descents:   Tolerance (Fmax)   =  1.0e+00   Number of steps    = &
 #160;    200Step=    0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom= 26Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06,  ^^^atom= 26Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1Double precision normally gives you higher accuracy.writing lowest energy coordinates.Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax < 1.Potential Energy  =  1.0667836e+05Maximum for
 ce =  3.6336775e+06 on atom 26Norm of force =    nan___2. in the full MD simulation, the "warning" coming, the messages is:Step 0, time 0 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:max 0.881911 (between atoms 27 and 28) rms nanbonds that rotated more than 30 degrees: atom 1 atom 2  angle  previous, current, constraint length 27 28   90.0    0.1610   0.3030  0.1610Wrote pdb files with previous and current coordinatesstep 2490, remaining runtime: 0 s   &
 #160;   Writing final coordinates.Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#step 2500, remaining runtime: 0 s   __And in the ".gro" file after this step, the coordinates of all atoms are "nan". So it means there are crash in the structure? Is the crash between the atom 27 and 28? How to modify the structure file make it normal?Thank you very much!Duan<[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]><[EMAIL PROTECTED]>>MoJie Duan wrote:> >  >So look at your structures like I said last time! I'm not her
 e to give> >  >my valuable time giving free advice in order to have it ignored...> > Thank you very much for your kindness and patience. Maybe sometimes my > > questions seems to be silly and boring, my knowledge about GROMACS is > >really lack, sorry.> > >Actually, I really cannot understand what you said yesterday. Did you > >mean is there any difference between the atom coordinates of ATP before- > >and after- minimization?> There would normally be some differences visible. If your topology was> badly broken, then you would usually see where it was broken.>  >I found there are not any difference between > >these two structure.> >(There are also not any obvious collision between atoms of ATP when > >represent it by Rasmol)> OK, so that means your structure is in a flat area of 
 the potential> surface defined by your topology. If the topology is sound, then you're> in business.> My first recommendation was to minimize and/or equilibrate these> structures on their own, and now I suggest doing them also in solvent.> This will help you eliminate sources of problems and guide you to > what the real problem is. Divide and conquer...> That's fine, then.> OK, so here's your problem. Work out what's breaking and why. Read the> error messages and look at the structures. Understand what each of  > your .mdp file options does.Mark 

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Re: [gmx-users] GAP parameter

[Osmair Vital de Oliveira]

Dear Mark,

Thank you and sorry. From parameters of oplsaa and quantum calculations, I
have been building  all force field parameters for GAP.

Cheers


On Fri, 17 Aug 2007, Mark Abraham wrote:

> Osmair Vital de Oliveira wrote:
> > Dear Mark,
> >
> > Thank you for the helpful!!. For instance, I have been working with
> > molecular dynamics simulation using gromacs for five years...
> > Therefore, my ask is an thoughtful question. Contrary with your
> > answer..
>
> You didn't technically ask a question :-) In order to maximise your
> chances of getting free help, you don't need to be ingratiating, but you
> should be trying to show respect for your readers' time and expertise by
> expressing yourself clearly. An email like
>
> "Hi, I've been doing molecular dynamics with GROMACS for five years and
> want to simulate system . I know I could generate a topology for
> D-glyceraldehyde-3-phosphate for forcefield  by hand, but was
> wondering whether anybody in the GROMACS community has one already
> they'd be willing to share?"
>
> Now people know exactly what you want and why, and might answer
>
> "Yes, but only for forcefield "
>
> "No, and by the way, forcefield  might be superior for  reasons>"
>
> "No, but  published a simulation in journal  with a similar
> molecule and you could try contacting them"
>
> "No, but you could check out
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
> http://wiki.gromacs.org/index.php/Parameterization for some advice on
> generating topologies."
>
> ... and they'd be more motivated to give such thoughtful help if they
> get a thoughtful question.
>
> Cheers :-)
>
> Mark
>
> > On Fri, 17 Aug 2007, Mark Abraham wrote:
> >
> >> Osmair Vital de Oliveira wrote:
> >>> Hi,
> >>>
> >>> Somebody has force field parameters of the D-glyceraldehyde-3-phosphate
> >>> (GAP).
> >> If you want to ask a question, please ask an thoughtful question. You
> >> should probably also check out
> >> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
> >> http://wiki.gromacs.org/index.php/Parameterization
> >>
> >> Mark
> ___
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[gmx-users] how to get CVS version gmx?

[Zhaoyang Fu]

Dear gmx users & developers,

  Would you please let me know how to get the gmx CVS version? I
registered in gmx website, however, everytime I try to view the link
"*instructions
on how to access our CVS
repository*",
it always says 'You are not authorised to view this resource'.

Since gmx3.3.1 has bug in trjconv program, I would like to get the cvs
version, which has fixed this problem.

Thanks in advance!

Linda
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Re: [gmx-users] The energy minimization....

[TJ Piggot]

Hi you need to explain in detail what steps you are doing before the 
minimisation and also what parameters you are using in your .mdp file 
because i have just run a minimisation of ATP (in water) to test the 
topology in the GROMOS96 ff and it works fine for me, so there must be a 
problem in one of your setup steps or your simulation parameters.


Tom

--On Friday, August 17, 2007 18:15:40 +0800 MoJie Duan 
<[EMAIL PROTECTED]> wrote:



Hi, Mark:
I have done the energy minimization and simulation of ATP in vacuum
individual ( Maybe you have suggested me to do this yesterday, but
actually I did not understand it, and just do this in solution).
There are following problems:
1. in the energy minimization, the potential energy is positive and in
14th step, it's potential energy is "nan". But the ".gro" outfile of
"mdrun" is just the same as the original file (i.e. the .gro file before
minimization), the return messages of mdrun is (there are not any
warning):

--
Getting Loaded...
Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps    = & #160;    200
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom=
26
Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06,
 ^^^
atom= 26
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy  =  1.0667836e+05
Maximum for ce =  3.6336775e+06 on atom 26
Norm of force =    nan
___

2. in the full MD simulation, the "warning" coming, the messages is:


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.881911 (between atoms 27 and 28) rms nan
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
 27 28   90.0    0.1610   0.3030  0.1610
Wrote pdb files with previous and current coordinates
step 2490, remaining runtime: 0 s   & #160;   Writing final
coordinates.

Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
step 2500, remaining runtime: 0 s  
__

And in the ".gro" file after this step, the coordinates of all atoms are
"nan". So it means there are crash in the structure? Is the crash between
the atom 27 and 28? How to modify the structure file make it normal?
Thank you very much!

Duan



MoJie Duan wrote:
> > So look at your structures like I said last time! I'm not her e to
> > give my valuable time giving free advice in order to have it
> > ignored...
> Thank you very much for your kindness and patience. Maybe sometimes my
> questions seems to be silly and boring, my knowledge about GROMACS is
> really lack, sorry.

> Actually, I really cannot understand what you said yesterday. Did you
> mean is there any difference between the atom coordinates of ATP
> before-  and after- minimization?




There would normally be some differences visible. If your topology was
badly broken, then you would usually see where it was broken.



> I found there are not any difference between
> these two structure.
> (There are also not any obvious collision between atoms of ATP when
> represent it by Rasmol)



OK, so that means your structure is in a flat area of the potential
surface defined by your topology. If the topology is sound, then you're
in business.



My first recommendation was to minimize and/or equilibrate these
structures on their own, and now I suggest doing them also in solvent.
This will help you eliminate sources of problems and guide you to
what the real problem is. Divide and conquer...



That's fine, then.



OK, so here's your problem. Work out what's breaking and why. Read the
error messages and look at the structures. Understand what each of  >
your .mdp file options does.


Mark






--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] how to get CVS version gmx?

[Carsten Kutzner]

Hi Linda,

you can use these commands to download from CVS:


cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login

Then hit  on password prompt

cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co gmx


Carsten


Zhaoyang Fu wrote:
> Dear gmx users & developers,
>  
>   Would you please let me know how to get the gmx CVS version? I
> registered in gmx website, however, everytime I try to view the link "
> *instructions on how to access our CVS repository*
> ",
> it always says 'You are not authorised to view this resource'.
>  
> Since gmx3.3.1 has bug in trjconv program, I would like to get the cvs
> version, which has fixed this problem.
>  
> Thanks in advance!
>  
> Linda
> 
> 
> 
> 
> ___
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Re: [gmx-users] The energy minimization....

[Alan Dodd]

The end structure is the same as the start because gromacs cannot find a lower 
energy structure than the initial one.  This indicates something severely 
wrong, either with the topology or starting structure.  You could get a better 
idea of what's going on by telling gromacs to output structures every step in 
the minimisation, and examining these so you can actually observe what is 
happening to your ATP.
I've occasionally seen similar results from minimisation, but only after doing 
something REALLY bad, like precisely overlaying two molecules on the same 
coordinates.  Debugging something like this is probably something only you are 
going to be able to do, as there are just so many potential ways a suitably, 
uh, imaginative user can mess things up.  

- Original Message 
From: MoJie Duan <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Friday, August 17, 2007 11:15:40 AM
Subject: Re: [gmx-users] The energy minimization

Hi, Mark:
I have done the energy minimization and simulation of ATP in vacuum individual 
( Maybe you have suggested me to do this yesterday, but actually I did not 
understand it, and just do this in solution).
There are following problems:
1. in the energy minimization, the potential energy is positive and in 14th 
step, it's potential energy is "nan". But the ".gro" outfile of "mdrun" is just 
the same as the original file (i.e. the .gro file before minimization), the 
return messages of mdrun is (there are not any warning):

--
Getting Loaded...
Reading file ATP.2_min.tpr, VERSION 3.3.1 (single precision)
Loaded with Money


Back Off! I just backed up ATP.2_minrun.edr to ./#ATP.2_minrun.edr.1#
Steepest Descents:
   Tolerance (Fmax)   =  1.0e+00
   Number of steps= & #160;200
Step=0, Dmax= 1.0e-02 nm, Epot=  1.06678e+05 Fmax= 3.63368e+06, atom= 26
Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 3.63313e+06, 
 ^^^
atom= 26
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up ATP.2_minrun.gro to ./#ATP.2_minrun.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1.
Potential Energy  =  1.0667836e+05
Maximum for ce =  3.6336775e+06 on atom 26
Norm of force =nan
___

2. in the full MD simulation, the "warning" coming, the messages is:


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.881911 (between atoms 27 and 28) rms nan
bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length
 27 28   90.00.1610   0.3030  0.1610
Wrote pdb files with previous and current coordinates
step 2490, remaining runtime: 0 s   & #160;   Writing final 
coordinates.

Back Off! I just backed up ATP.2_runout.gro to ./#ATP.2_runout.gro.1#
step 2500, remaining runtime: 0 s   
__

And in the ".gro" file after this step, the coordinates of all atoms are "nan". 
So it means there are crash in the structure? Is the crash between the atom 27 
and 28? How to modify the structure file make it normal?
Thank you very much!

Duan


>MoJie Duan wrote:
> > >So look at your structures like I said last time! I'm not her e to give
> > >my valuable time giving free advice in order to have it ignored...
> > Thank you very much for your kindness and patience. Maybe sometimes my 
> > questions seems to be silly and boring, my knowledge about GROMACS is 
> >really lack, sorry.
> 
> >Actually, I really cannot understand what you said yesterday. Did you 
> >mean is there any difference between the atom coordinates of ATP before- 
> >and after- minimization?


> There would normally be some differences visible. If your topology was
> badly broken, then you would usually see where it was broken.

> >I found there are not any difference between 
> >these two structure.
> >(There are also not any obvious collision between atoms of ATP when 
> >represent it by Rasmol)

> OK, so that means your structure is in a flat area of the potential
> surface defined by your topology. If the topology is sound, then you're
> in business.

> My first recommendation was to minimize and/or equilibrate these
> structures on their own, and now I suggest doing them also in solvent.
> This will help you eliminate sources of problems and guide you to 
> what the real problem is. Divide and conquer...

> That's fine, then.

> OK, so here's your problem. Work out what's breaking and why. Read the
> error messages and look at the structures. Understand what each of  > your 
> .mdp file optio

[gmx-users] Generalized order parameter S2

[Dilraj Lama]

Hello gmx-users,
   I have a query regarding the generalized order paprameter
S2.I have performed a 50ns simulation of a protein in
solution.I now want to calculate the order parameter S2 of
the protein from the trajectory.I looked through the
mailing list to get an idea on how to go about calculating
the property.

I collected information that the tools "g_chi" and "g_rotacf" can help me
perform the task.

g_chi uses Phi, Psi and Omega angles to calculate it.

g_rotacf can calculate it with respect to N-H bond angle.

Which of the two approach would be more appropriate?

Also using "g_rotacf" I am still not very clear on how to go about using
the  tool.

Can anyone who has previuosly performed this calculation help me out.

I look forward to your responses.

Thank you.


-- 
Dilraj Lama,
Graduate student,
Bioinformatics and Biomolecular Simualtion lab,
Dept. of BSBE;IITK-kanpur,
Uttar pradesh,India-208016.
email:[EMAIL PROTECTED],[EMAIL PROTECTED]
mob:09415473973

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[gmx-users] Re : long-term drift and crash

[BON Michael]

The same bugs occurs during the NPT equilibration stage that I did after the 
energy minimization (with l-bgfs, till convergence), the average pressure being 
now -0.5 bar (over the 200 ps the simulation ran before it crashed).
Still the same things : everything I plot with g_energy is normal, the msd plot 
oscillates more and more, I see nothing special on the last configuration just 
before the crash).
This really puzzles me.
Thanks for your help.
Michaël Bon

Message: 4
Date: Wed, 15 Aug 2007 14:58:54 +1000
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] RE : long-term drift and crash
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

BON Michael wrote:
> Hi and thanks,
> 
> The pressure is stable, the mean value is -280 bar, which sounds normal, and 
> it is isotropic (Pres-XX = Pres-YY = Pres-ZZ = -280 bar)

That value doesn't sound too normal to me, depending on the size of the 
fluctuations and the length of time over which you've measured that 
average, and/or whether the density is reasonable. Perhaps you should 
try an NPT equilibration stage as suggested here 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation, in 
order to fix the density.

> I also tried with no constraint (I forgot to mention it in my previous mail) 
> but it didn't solve anything.
> 
> I did a proper energy minimization, there is no warning, error message, wierd 
> energy at any moment. Moreover, I tried to simulate many different systems, 
> doing each time a good minimization, and I always get this strange behaviour.

Mark

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[gmx-users] Step size too small

[Sheyore Omovie]

Dear gmx-users,
 
I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the 
.top file to remove the bonds created between the two molecules, I also added a 
distance restraint btw the molecules. (The 2 structures have been separately 
minimized). However, I get the ff message for EM run:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
 
Double precision normally gives you higher accuracy.
 
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.0246325e+20
Maximum force =inf on atom 1
Norm of force =inf
I would appreciate any advice on how to fix this.
Rgds
John
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Re: [gmx-users] Step size too small

[Per Larsson]

Hello!

Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 
2C_or_no_change_in_energy._Converged_to_machine_precision. 
2C_but_not_to_the_requested_precision


Cheers
/Per

17 aug 2007 kl. 18.28 skrev Sheyore Omovie:


Dear gmx-users,

I have 2 molecules in a box, as usual pdb2gmx saw them as one. i  
edited the .top file to remove the bonds created between the two  
molecules, I also added a distance restraint btw the molecules.  
(The 2 structures have been separately minimized). However, I get  
the ff message for EM run:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.0246325e+20
Maximum force =inf on atom 1
Norm of force =inf
I would appreciate any advice on how to fix this.
Rgds
John

See what you’re getting into…before you go there See it!
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Re: [gmx-users] Pull code methods?

[bmmothan]

Hi Maik,

Thank you for the answer. I still have some questions.

I still didn't get the umberalla sampling method. It seems to me AFM and
umberalla are the same except that in umberalla we dont define a Pull
rate. Looking at the literature, people have been using umberalla method
with discrete simulations. i.e. 21 simulation windows. I kind of get the
idea that you will have to manually set up the the 21 discrete simulations
to get the final separated ligand-protein for the umberalla method?
correct me if I am wrong.


The other question I had is about init-afm position option. it says in the
manual:
afm init1 =
Vector describing the initial position of the spring relative to the
reference group. To start a simulation with zero initial force on the
pulled group, the initial position should be set to the position of the
pulled group relative to the reference group.


This sentence is very unclear to me. how do u calculated the poition of
the pulled group relative to the referene.  Is is by calculating the
Center of mass of the pulled group or by calculating the center of mass of
the the whole system (pulled group + reference)?

Thank you,

Belquis



> Hi
>
> You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF
> you want to calculate (runtype=afm,umbrella). Depending on this choice
> it's very likely that the afm_rate is simply ignored for umbrella, no?
>
> The force constant is mimicking the stiffness of the spring. You want to
> obey the stiff spring approximation (which still does NOT mean, you
> should use a rod ;) ) and therefore shouldn't choose the fc of the
> spring to small. I usually use a force constant of 500 kJ/mol*nm^2.
> It actually DOES make sense, to choose a fc comparable to the
> experiments, you want to compare your sim with, IF you want to compare :)
>
> Hope that helps
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>  mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> [EMAIL PROTECTED] wrote:
>> Dear all,
>>
>> I have been reading the literature, mailing list and the manual.
>>
>> There is some questions that I cant understand:
>>
>> 1) there is three methods for the pull code: constraint force, AFM and
>> umberalla.
>>
>> in both AFM and Constraint force, there is an option of the rate of
>> pulling (contraint_rate, AFM_rate), however, for umberalla, there is
>> only
>> two options, a foce constant and position to be specified!
>> my question is: how is the pulling controlled in umberalla sampling
>> option?
>>
>> 2) if I want to do an AFM pulling...what is a reasonalble force
>> constant
>> to use? it seems people are using different K ranging from 10 to
>> 1000's?
>>
>> thank u
>>
>> Belquis
>>
>> ___
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Re: [gmx-users] Step size too small

[TJ Piggot]

Hi,

I do not think that what Per suggests is the problem, if you look at the 
potential energy after the minimisation this value is huge (and the other 
two values are inf!). The problem is most likely with your topology. As you 
say the two molecules have been successfully minimised on their own so I 
would suggest that your problem is with either how you edit the .top file 
or the distance restraint between the molecules. For my protein that has 
more than one identical chains pdb2gmx does not recognise them as one if 
you provide different chain identifiers in the pdb file, so doing this 
should hopefully stop you having to edit the .top file.


Hope this helps

Tom

--On 17 August 2007 19:02 +0200 Per Larsson <[EMAIL PROTECTED]> wrote:


Hello!


Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan
ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_
precision


Cheers
/Per



17 aug 2007 kl. 18.28 skrev Sheyore Omovie:

 Dear gmx-users,
  
 I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited
the .top file to remove the bonds created between the two molecules, I
also added a distance restraint btw the molecules. (The 2 structures have
been separately minimized). However, I get the ff message for EM run:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
 
Double precision normally gives you higher accuracy.
 
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.0246325e+20
Maximum force =    inf on atom 1
Norm of force =    inf I would appreciate any advice on how
to fix this.
 Rgds
 John


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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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[gmx-users] Pressure coupling and tau_p values

[toma0052]

Hello,
 I am simulating a lipid bilayer system under a shear stress, in which I
am interested in looking at the surface tension.  I have done a number of
simulations in an NPT ensemble using semiisotropic Berendsen pressure
coupling.  For a system such as this, I am wondering what would be an optimal
tau_p because I seem to be getting slightly different results dependent on
the value I choose.  For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.  Is this difference negligible?
 I have looked into this a bit, and I have seen a number of publications
in which people have used Berendsen pressure coupling in a lipid bilayer
system with a coupling constant of 0.5 or 1.0ps.  However, in the mailing
list, there are some posts in which it is recommended that one use a tau_p of
5.0ps to 10.0ps due to semiisotropic coupling not having the averaging effect
of isotropic coupling and using a small coupling time can add excessive noise
to the system.  Therefore, is it more reliable when simulating a lipid
bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps? 

Thank you,
Mike Tomasini

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[gmx-users] job magic number in MXMPI_MAGIC

[Sheyore Omovie]

Thanks Tom,
I have tried that in the past though, and I still get Epot values of nan.
It seems the only other option I have is to place the molecules in separate 
boxes, set 
disre=simple, and use the -multi option during the mdrun. The -multi option 
only works with the parallel installation.
Unfortunately I get the ff error message when I try to use the parallel gromacs 
installation on the server:
 Error: Need to obtain the job magic number in MXMPI_MAGIC.
I would appreciate any advice on how to fix this.
Rgds
John
> Date: Fri, 17 Aug 2007 20:46:58 +0100> From: [EMAIL PROTECTED]> To: 
> gmx-users@gromacs.org> Subject: Re: [gmx-users] Step size too small> > Hi,> > 
> I do not think that what Per suggests is the problem, if you look at the > 
> potential energy after the minimisation this value is huge (and the other > 
> two values are inf!). The problem is most likely with your topology. As you > 
> say the two molecules have been successfully minimised on their own so I > 
> would suggest that your problem is with either how you edit the .top file > 
> or the distance restraint between the molecules. For my protein that has > 
> more than one identical chains pdb2gmx does not recognise them as one if > 
> you provide different chain identifiers in the pdb file, so doing this > 
> should hopefully stop you having to edit the .top file.> > Hope this helps> > 
> Tom> > --On 17 August 2007 19:02 +0200 Per Larsson <[EMAIL PROTECTED]> 
> wrote:> > > Hello!> >> >> > Check out> > 
> http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan> > 
> ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_> > 
> precision> >> >> > Cheers> > /Per> >> >> >> > 17 aug 2007 kl. 18.28 skrev 
> Sheyore Omovie:> >> > Dear gmx-users,> >  > > I have 2 molecules in a box, as 
> usual pdb2gmx saw them as one. i edited> > the .top file to remove the bonds 
> created between the two molecules, I> > also added a distance restraint btw 
> the molecules. (The 2 structures have> > been separately minimized). However, 
> I get the ff message for EM run:> >> > Stepsize too small, or no change in 
> energy.> > Converged to machine precision,> > but not to the requested 
> precision Fmax < 1000> >  > > Double precision normally gives you higher 
> accuracy.> >  > > Steepest Descents converged to machine precision in 15 
> steps,> > but did not reach the requested Fmax < 1000.> > Potential Energy  = 
>  1.0246325e+20> > Maximum force =inf on atom 1> > Norm of 
> force =inf I would appreciate any advice on how> > to fix 
> this.> > Rgds> > John> >> >> > 
> __> > See what you’re getting 
> into?before you go there See it!> > 
> ___> > gmx-users mailing list
> gmx-users@gromacs.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/mailing_lists/users.php> >> >> > > > 
> --> TJ Piggot> [EMAIL PROTECTED]> University of Bristol, 
> UK.> > ___> gmx-users mailing 
> list gmx-users@gromacs.org> 
> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive 
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[gmx-users] Re: \[gmx\-users\] The energy minimization\.\.\.\. (fwd)

[TJ Piggot]

Hi

Also please keep emails on the list, it helps everyone (you getting more 
people's opinion than just mine, and people who may have a similar problem 
in the future)


Tom

 Forwarded Message 
Date: 18 August 2007 02:29 +0100
From: TJ Piggot <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: Re: \[gmx\-users\] The energy minimization\.\.\.\.

Hi

I just quickly checked and your ATP pdb file works fine for me (it did have
some weird characters in it that i had to delete, not sure if this was
caused by pasting it into an email). I should point out that this pdb file
is incomplete as you are missing some hydrogen atoms (pdb2gmx should tell
you this if you modified your .rtp file correctly). See any of the GROMOS96
.rtp file ATP entries for the hydrogens you have missed that still are
included in a united atom ff.

Also your .mdp parameters work fine with your pdb file so i have no idea
what is going wrong when you try! Check you have modified the .rtp file
correctly and are supplying sensible commands to
pdb2gmx/editconf/grompp/mdrun are the last things i can suggest.

Good luck

Tom

--On 18 August 2007 08:17 +0800 MoJie Duan <[EMAIL PROTECTED]> wrote:


Hi,Tom:
Thank you for your reply!
Before the minimization, I just change the atoms name of ATP, so it can
coordinated to the names in ffG43b1 (the atoms name of ATP in ffG43b1
also changed, each atom have a three-letter name).

My coordinate file (.pdb) was obtained from RCSB PDB, I extracted the xyz
coordinates of ATP molecule from the a .pdb file of a protein, as
following:
___
HETATM 7577  PG  ATP   800  -4.997   4.425  -2.604  1.00
33.08   P 
HETATM 7578  O1G ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  O2G ATP   800  -3.427   4.765  -2.665  1.00 32.63  
0;    O 
HETATM 7580  O3G ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  PB  ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  O1B ATP   800  -3.985   4.318  -6.120  1.00
33.33   O 
HETATM 7583  O2B ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  O3B ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  PA  ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  O1A ATP   800  -8.260   2.720  -5.177  1.00
33.60   O 
HETATM 7587  O2A ATP   800  -7.501   2.503  -7.632  1.00
32.64   O 
HETATM 7588  O3A ATP   800  -6.483   4.274  -6.168  1.00
34.07   O 
HETATM 7589  O5' ATP   800  -8.787   4.518 0; -6.833  1.00
36.40   O 
HETATM 7590  C5' ATP   800  -8.403   5.464  -7.846  1.00
39.10   C 
HETATM 7591  C4' ATP   800  -9.604   6.315  -8.269  1.00
41.61   C 
HETATM 7592  O4' ATP   800 -10.793   5.471  -8.462  1.00
42.22   O 
HETATM 7593  C3' ATP   800  -9.937   7.303  -7.152  1.00
41.81   C 
HETATM 7594  O3' ATP   800 -10.228   8.5 59  -7.756  1.00
43.61   O 
HETATM 7595  C2' ATP   800 -11.191   6.724  -6.514  1.00
42.05   C 
HETATM 7596  O2' ATP   800 -12.023   7.764  -6.036  1.00
41.49   O 
HETATM 7597  C1' ATP   800 -11.875   6.025  -7.679  1.00
42.90   C 
HETATM 7598  N9  ATP   800 -12.608   4.832  -7.218  1.00
43.53   N 
HETATM 7599  C8  ATP   800 -12.077   3. 810  -6.547  1.00
43.35   C 
HETATM 7600  N7  ATP   800 -13.023   2.904  -6.309  1.00
44.02   N 
HETATM 7601  C5  ATP   800 -14.162   3.341  -6.835  1.00
44.22   C 
HETATM 7602  C6  ATP   800 -15.461   2.828  -6.899  1.00
44.02   C 
HETATM 7603  N6  ATP   800 -15.751   1.647  -6.351  1.00
43.35   N 
HETATM 7604  N1  ATP   800 -16.41 4   3.547  -7.525  1.00
43.25   N 
HETATM 7605  C2  ATP   800 -16.125   4.717  -8.076  1.00
43.37   C 
HETATM 7606  N3  ATP   800 -14.902   5.230  -8.032  1.00
43.76   N 
HETATM 7607  C4  ATP   800 -13.901   4.571  -7.417  1.00
44.09   C


and then changed the atoms name:


HETATM 7577  APG ATP   800  -4.997   4.425  -2.604& #160; 1.00
33.08   P 
HETATM 7578  OG1 ATP   800  -5.685   5.603  -1.764  1.00
33.76   O 
HETATM 7579  OG2 ATP   800  -3.427   4.765  -2.665  1.00
32.63   O 
HETATM 7580  OG3 ATP   800  -5.273   3.100  -1.967  1.00
33.16   O 
HETATM 7581  APB ATP   800  -5.173   3.787  -5.388  1.00
34.37   P 
HETATM 7582  OB1 ATP   800  -3.985   4.3 18  -6.120  1.00
33.33   O 
HETATM 7583  OB2 ATP   800  -5.232   2.335  -5.045  1.00
33.33   O 
HETATM 7584  OB3 ATP   800  -5.529   4.675  -4.089  1.00
33.22   O 
HETATM 7585  APA ATP   800  -7.773   3.348  -6.436  1.00
35.04   P 
HETATM 7586  OA1 ATP   800  -8.260   

Re: [gmx-users] job magic number in MXMPI_MAGIC

[Mark Abraham]

Sheyore Omovie wrote:

Thanks Tom,
I have tried that in the past though, and I still get Epot values of nan.


One solution is to take your (successful) individual .top files and edit 
them in line with the example in chapter 5 to create .itp files for your 
two molecules. Then include them both in a master .top, set up a 
structure file with both molecules and use editconf and genbox and 
grompp in the usual way.


It seems the only other option I have is to place the molecules in 
separate boxes, set
disre=simple, and use the -multi option during the mdrun. The -multi 
option only works with the parallel installation.


-multi allows you to do multiple independent simulations. This won't do 
anything differently for you than doing the independent simulations 
asynchronously.


Unfortunately I get the ff error message when I try to use the parallel 
gromacs installation on the server:

/ Error: Need to obtain the job magic number in MXMPI_MAGIC./
/I would appreciate any advice on how to fix this./


This is an MPI problem, not a GROMACS problem. Consult your sysadmins.

Mark
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Re: [gmx-users] Re : long-term drift and crash

[Mark Abraham]

BON Michael wrote:

The same bugs occurs during the NPT equilibration stage that I did after the 
energy minimization (with l-bgfs, till convergence), the average pressure being 
now -0.5 bar (over the 200 ps the simulation ran before it crashed).
Still the same things : everything I plot with g_energy is normal, the msd plot 
oscillates more and more, I see nothing special on the last configuration just 
before the crash).


Actually that link suggests some NVT to fix temperatures and NPT to fix 
box size. It sounds like your system is fragile and you should be doing 
both of these... or at least telling us that you're doing both of these.


Mark
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[gmx-users] Pressure coupling and tau_p values

[chris . neale]

For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.


First thing that comes to mind is that your area per lipid is not at  
equilibrium. Assuming that your bilayer normal lies in the Z  
dimension, plot your xy area vs. simulation time. My bet is that it is  
not converged and that the run using a tau_p of 0.5 is approaching  
convergence faster than the run using a tau_p of 5.0. Once it is  
converged, I would recommend something more like 20ns for a production  
run.



Is this difference negligible?


Test that out yourself. Do some repeats, or perhaps take the 3ns  
snapshot from the simulation at tau_p of 0.5 and continue it using a  
tau_p of 5.0. Also take the 3ns snapshot from the simulation at tau_p  
of 5.0 and continue it using a tau_p of 0.5.



Therefore, is it more reliable when simulating a lipid
bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps?


Sorry, I don't know the answer to that one.

Chris.

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