Re: [gmx-users] minimization of particular residue/atom

[Mark Abraham]

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 wrote:

> 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, but
> can be y or z). So mdrun was complaining one by one and I edited in all
> three such x coordinates for three atoms. finally I was able to achieve
> convergence.
>
> I believe moving just 0.1 nm minimization will take care of correct
> lengths. May be if its not the correct way; please suggest.
>
> regards,
>
>
> On Thu, May 2, 2013 at 12:50 AM, Mark Abraham  >wrote:
>
> > On Wed, May 1, 2013 at 4:20 PM, gromacs query  > >wrote:
> >
> > > 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)
> > >
> >
> > All the above means your system is
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> >
> > I removed the  full lipid residue having atom number 4281. I was again
> > > getting error representing some other atoms so finally I removed three
> > > lipid residues. Doing this I was able to complete convergence.
> > >
> > > I have two queries:
> > >
> > > 1) As I have removed three residues from Charmm gui membrane, does this
> > > affect final results? Although I will be doing MD for membrane first.
> > >
> >
> > Maybe. We don't know whether the membrane was built wrongly, or you
> > post-processed the coordinate file wrongly, or whether you need all the
> > lipid molecules to achieve the right density, or...
> >
> >
> > > 2) Also is there any way so that particular atoms can be minimized or
> > > ''touched'' ? Here in this case I removed three lipid residues but this
> > > will not be good say in case of proteins. Just as a analogy if this
> > problem
> > > arises  in AMBER (rather I faced such problem many times) I can use
> xleap
> > > and can move atom a little and relax it particularly by selecting it ,
> so
> > > that later if use the edited structure I get convergence properly
> without
> > > error.
> > >
> >
> > You can only do that by moving the coordinates by hand in the coordinate
> > file before you give it to grompp. Your PE above is so large that this is
> > not the right approach to fix the problem. I would guess your periodic
> box
> > is not the one you were intended to use.
> >
> > Mark
> >
> >
> > >
> > > regards,
> > > Jio
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
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> > >
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Re: [gmx-users] minimization of particular residue/atom

[gromacs query]

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, but
can be y or z). So mdrun was complaining one by one and I edited in all
three such x coordinates for three atoms. finally I was able to achieve
convergence.

I believe moving just 0.1 nm minimization will take care of correct
lengths. May be if its not the correct way; please suggest.

regards,


On Thu, May 2, 2013 at 12:50 AM, Mark Abraham wrote:

> On Wed, May 1, 2013 at 4:20 PM, gromacs query  >wrote:
>
> > 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)
> >
>
> All the above means your system is
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> I removed the  full lipid residue having atom number 4281. I was again
> > getting error representing some other atoms so finally I removed three
> > lipid residues. Doing this I was able to complete convergence.
> >
> > I have two queries:
> >
> > 1) As I have removed three residues from Charmm gui membrane, does this
> > affect final results? Although I will be doing MD for membrane first.
> >
>
> Maybe. We don't know whether the membrane was built wrongly, or you
> post-processed the coordinate file wrongly, or whether you need all the
> lipid molecules to achieve the right density, or...
>
>
> > 2) Also is there any way so that particular atoms can be minimized or
> > ''touched'' ? Here in this case I removed three lipid residues but this
> > will not be good say in case of proteins. Just as a analogy if this
> problem
> > arises  in AMBER (rather I faced such problem many times) I can use xleap
> > and can move atom a little and relax it particularly by selecting it , so
> > that later if use the edited structure I get convergence properly without
> > error.
> >
>
> You can only do that by moving the coordinates by hand in the coordinate
> file before you give it to grompp. Your PE above is so large that this is
> not the right approach to fix the problem. I would guess your periodic box
> is not the one you were intended to use.
>
> Mark
>
>
> >
> > regards,
> > Jio
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
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Re: [gmx-users] minimization of particular residue/atom

[Mark Abraham]

On Wed, May 1, 2013 at 4:20 PM, gromacs query wrote:

> 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)
>

All the above means your system is
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I removed the  full lipid residue having atom number 4281. I was again
> getting error representing some other atoms so finally I removed three
> lipid residues. Doing this I was able to complete convergence.
>
> I have two queries:
>
> 1) As I have removed three residues from Charmm gui membrane, does this
> affect final results? Although I will be doing MD for membrane first.
>

Maybe. We don't know whether the membrane was built wrongly, or you
post-processed the coordinate file wrongly, or whether you need all the
lipid molecules to achieve the right density, or...


> 2) Also is there any way so that particular atoms can be minimized or
> ''touched'' ? Here in this case I removed three lipid residues but this
> will not be good say in case of proteins. Just as a analogy if this problem
> arises  in AMBER (rather I faced such problem many times) I can use xleap
> and can move atom a little and relax it particularly by selecting it , so
> that later if use the edited structure I get convergence properly without
> error.
>

You can only do that by moving the coordinates by hand in the coordinate
file before you give it to grompp. Your PE above is so large that this is
not the right approach to fix the problem. I would guess your periodic box
is not the one you were intended to use.

Mark


>
> regards,
> Jio
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Minimization problem

[Justin Lemkul]

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 is a I/O issue?


You won't get a log file.  The -m flag is used only to print methods information 
from the .tpr file and is not relevant here.  An I/O issue is an input/output 
problem (i.e. reading/writing from/to the disk).  If it happens every time you 
run the minimization, that doesn't sound like it's relevant.


Is this reproducible with 4.6beta3?

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization problem

[Justin Lemkul]

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 gmxcheck -h :)  The -e flag reads in a .edr file and checks 
its integrity.  If you can verify that this problem still persists with version 
4.6beta3, then it may be worth a bug report to see what's going on.  Seems like 
there's an I/O issue.  Does it only affect double precision or single as well?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization problem

[Marcelo Depolo]

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
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Re: [gmx-users] Minimization problem

[Marcelo Depolo]

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.
-- 
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Re: [gmx-users] Minimization problem

[Justin Lemkul]

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: step=-1, nre=36, nblock=0, time=-1.
Trying to skip frame expect a crash though"*

Anyone knows about this particular error message?


What version of Gromacs are you using?  What does gmxcheck tell you about the 
.edr file?  Is the problem reproducible, or did it happen just once?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization problem

[Elton Carvalho]

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 file prt_cg.edr
> Found: step=-1, nre=36, nblock=0, time=-1.
> Trying to skip frame expect a crash though"*
>
> Anyone knows about this particular error message?
> Thanks!


Sorry, I missed that part.

The minimization really stops because of the small stepsize. The
warning you mentioned is probably not directly related to mdrun
stopping.

What's your nstenergy value set in the mdp file?

--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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Re: [gmx-users] Minimization problem

[Marcelo Depolo]

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 skip frame expect a crash though"*

Anyone knows about this particular error message?
Thanks!
-- 
Marcelo Depólo Polêto
Molecular Animal Infectology Laboratory - LIMA
Department of Biochemistry and Molecular Biology
Universidade Federal de Viçosa - UFV - Brazil
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Re: [gmx-users] Minimization problem

[Elton Carvalho]

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 on atom 3684
>F-Norm=  2.99917e+02
>
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 0.1
>
> WARNING: there may be something wrong with energy file prt_cg.edr
> Found: step=-1, nre=36, nblock=0, time=-1.
> Trying to skip frame expect a crash though*
>

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil
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Re: [gmx-users] minimization force criteria

[Justin Lemkul]

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 precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 15318 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -3.3397742e+06
Maximum force =  9.8232233e+02 on atom 6057
Norm of force =  3.6321018e+00


Then according to the above instruction I increased the stepsize up to
0.5 [ I didn't use any constraint during minimization] but got the
same. So do I need to increase the stepsize more or is there other
procedure to get to the desired convergence criteria ?
The minimization .mdp file is as follows



Have you consulted the following?

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

It may simply not be possible to energy minimize the system further without 
using double precision or a better EM algorithm.  Steepest descents converges 
very quickly but the results can often be improved by additional rounds of CG or 
L-BGFS minimization.  For most purposes, one does not require such a low maximum 
force, but if you need Fmax < 10, then you likely need a significantly more 
robust protocol.


-Justin



; 7.3.2 Preprocessing
;define  = -DFLEXIBLE; defines to pass to the preprocessor

; 7.3.3 Run Control
integrator  = steep ; steepest descents energy minimization
nsteps  = 10 ; maximum number of steps to integrate

; 7.3.5 Energy Minimization
emtol   = 10; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep  = 0.01   ; [nm] initial step-size
nstcgsteep  = 10;  freq of performing one
steepest descent step

; 7.3.8 Output Control
nstxout = 500   ; [steps] freq to write
coordinates to trajectory
nstvout = 500   ; [steps] freq to write
velocities to trajectory
nstfout = 500   ; [steps] freq to write forces
to trajectory
nstlog  = 100   ; [steps] freq to write
energies to log file
nstenergy   = 100   ; [steps] freq to write
energies to energy file
energygrps  = System; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist = 1 ; [steps] freq to update neighbor list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions
in all directions
rlist   = 0.8   ; [nm] cut-off distance for
the short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 0.8   ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype = cut-off   ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw= 0.8   ; [nm] distance for LJ cut-off
DispCorr= Ener  ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing for FFT
grid when using PME
pme_order   = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb


Thanks,

Tarak



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization with DPOSRE

[Justin A. Lemkul]

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 change their positions. Thus, when I
want to run NVT equilibration I got errors of water molecules which cannot be
settled so EM is needed. Would you advise something?



Restraints do not guarantee that atoms won't move.  They are simply a biasing 
force that disfavors motion.  Either apply a stronger force constant for the 
restraints or use freezegrps to fix the atomic positions.


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization Problems

[Mark Abraham]

On 2/02/2012 3:42 PM, lina wrote:

On Thu, Feb 2, 2012 at 12:36 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 interactions, with each of them approaching inf.

Can anyone find anything glaringly wrong with my .mdp?

Thanks,
Alex Seling

title = Minimization of alpha-synuclein
cpp = /lib/cpp -traditional
define = -DFLEXIBLE
integrator = sd
constraints = none
tinit = 0
dt = 0.001
nsteps = 100
emtol = 0.1
emstep = 0.1
nstcgsteep = 1000
bd-fric = 0
nstlog = 50
nstenergy = 1
gen_temp = 273
gb_epsilon_solvent = 78.3
implicit_solvent = GBSA
gb_algorithm = Still
nstcomm = 10
xtc_precision = 1000
gen_vel = yes
nstxtcout = 0
nstxout = 100
pbc = no
energygrps = system
nstfout = 0
nstvout = 0
niter = 20
nstlist = 10

it's more about your .gro file (system), less about the .mdp file.


Can be either. Integration from a silly starting point (.gro) can be 
unstable, as can integration of a silly Hamiltonian (partly due to .mdp).


Mark
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Re: [gmx-users] Minimization Problems

[Mark Abraham]

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 interactions, with each of them approaching inf.


The usual advice and diagnostic procedure can be found here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up




Can anyone find anything glaringly wrong with my .mdp?


No constraints often requires a time step of 0.0005ps.

Mark



Thanks,
Alex Seling

title = Minimization of alpha-synuclein
cpp = /lib/cpp -traditional
define = -DFLEXIBLE
integrator = sd
constraints = none
tinit = 0
dt = 0.001
nsteps = 100
emtol = 0.1
emstep = 0.1
nstcgsteep = 1000
bd-fric = 0
nstlog = 50
nstenergy = 1
gen_temp = 273
gb_epsilon_solvent = 78.3
implicit_solvent = GBSA
gb_algorithm = Still
nstcomm = 10
xtc_precision = 1000
gen_vel = yes
nstxtcout = 0
nstxout = 100
pbc = no
energygrps = system
nstfout = 0
nstvout = 0
niter = 20
nstlist = 10




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Re: [gmx-users] Minimization Problems

[lina]

On Thu, Feb 2, 2012 at 12:36 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 interactions, with each of them approaching inf.
>
> Can anyone find anything glaringly wrong with my .mdp?
>
> Thanks,
> Alex Seling
>
> title = Minimization of alpha-synuclein
> cpp = /lib/cpp -traditional
> define = -DFLEXIBLE
> integrator = sd
> constraints = none
> tinit = 0
> dt = 0.001
> nsteps = 100
> emtol = 0.1
> emstep = 0.1
> nstcgsteep = 1000
> bd-fric = 0
> nstlog = 50
> nstenergy = 1
> gen_temp = 273
> gb_epsilon_solvent = 78.3
> implicit_solvent = GBSA
> gb_algorithm = Still
> nstcomm = 10
> xtc_precision = 1000
> gen_vel = yes
> nstxtcout = 0
> nstxout = 100
> pbc = no
> energygrps = system
> nstfout = 0
> nstvout = 0
> niter = 20
> nstlist = 10

it's more about your .gro file (system), less about the .mdp file.

>
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Re: [gmx-users] Minimization error

[Mark Abraham]

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 > 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 the minimization
but when visualised the pdb file after the minimization the
chains of the protein complex separated.

What could be the reason.


Please see FAQ #3 under the heading:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

-Justin


Thanks,
Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's
No. 1 Network. Go for it!


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin








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Re: [gmx-users] Minimization error

[aiswarya pawar]

Hi,

All the parameters are ok, still i get the complex separated.


On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul  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 the minimization but when visualised the pdb
>> file after the minimization the chains of the protein complex separated.
>>
>> What could be the reason.
>>
>>
> Please see FAQ #3 under the heading:
>
> http://www.gromacs.org/**Documentation/FAQs#Analysis_**and_Visualization
>
> -Justin
>
>
>  Thanks,
>> Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1
>> Network. Go for it!
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
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Re: [gmx-users] Minimization error

[Justin A. Lemkul]

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.



Please see FAQ #3 under the heading:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

-Justin


Thanks,
Aiswarya 
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Minimization error

[mu xiaojia]

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,  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.
>
> Thanks,
> Aiswarya
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] minimization problem (Martini simulation)

[politr]

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 with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01


This was the information I wanted to see.  Without it, no one had  
any idea if your EM converged reasonably.



Everything seems ok.


Indeed it does.


After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011

Step Time Lambda
0 0.0 0.0

Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03


Here's your problem.  The initial temperature is ridiculously small,  
indicating something has gone wrong.



Cons. rmsd ()
4.25390e-06

DD step 9 load imb.: force 3.0%

---
Program mdrun_mpi, VERSION 4.0.3


Any reason you're using a really old version of Gromacs?



Here's your problem.  The combination of:


tcoupl   = Berendsen


and


gen_vel  = no


is generally not stable.  You should set "gen_vel = yes" to start a  
reasonable equilibration period.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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This message was sent using IMP, the Internet Messaging Program.
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Re: [gmx-users] minimization problem (Martini simulation)

[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 with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01


This was the information I wanted to see.  Without it, no one had any idea if 
your EM converged reasonably.



Everything seems ok.


Indeed it does.


After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011

Step Time Lambda
0 0.0 0.0

Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03


Here's your problem.  The initial temperature is ridiculously small, indicating 
something has gone wrong.



Cons. rmsd ()
4.25390e-06

DD step 9 load imb.: force 3.0%

---
Program mdrun_mpi, VERSION 4.0.3


Any reason you're using a really old version of Gromacs?



Here's your problem.  The combination of:


tcoupl   = Berendsen


and


gen_vel  = no


is generally not stable.  You should set "gen_vel = yes" to start a reasonable 
equilibration period.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] minimization problem (Martini simulation)

[politr]

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
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01
Everything seems ok.
After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011

Step Time Lambda
0 0.0 0.0

Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03
Cons. rmsd ()
4.25390e-06

DD step 9 load imb.: force 3.0%

---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

---

"Step Aside, Butch" (Pulp Fiction)

I found that this error is connected to problems with minimization but  
unfortunately I don't know how to fix it.

I will appreciate very much any help.
Thank you.
Regina
mdp file used:
; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.030
nsteps   = 4000
; number of steps for center of mass motion removal =
nstcomm  = 1
; Groups for center of mass motion removal
comm-grps= System

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1000
nstenergy= 100
; Output frequency and precision for xtc file =
nstxtcout= 0
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =  Protein_PSE W_ION

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = Protein_PSE W_ION
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0  1.0
ref_t= 300  300
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5.0 5.0
compressibility  = 3e-4 3e-4
ref_p= 1.0 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = no
gen_temp = 300
gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30


Quoting "Justin A. Lemkul" :




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 following error:

Converged to machine precision,
but not to the requested precision Fmax < 10


This is not really an error:

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_

Re: [gmx-users] minimization problem (Martini simulation)

[Justin A. Lemkul]

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 following error:

Converged to machine precision,
but not to the requested precision Fmax < 10


This is not really an error:

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

The success of any subsequent MD depends on the magnitude of the maximum force 
the EM procedure achieved.  Minimizing to such a low force is very difficult and 
may not be possible for all systems.


I tried to use a bigger emtol(emtol=20) and it still didn't 
converge.However I still run the MD with dt = 0.03 and nstxout = 1. 
after something like 100 steps the system blow up.


Perhaps your EM wasn't sufficient, but based on the information you've posted, 
it's hard to draw any real conclusion about that.



I will appreciate any help with this issue.
Many thanks in advance.
P.S May it help if I minimize a smaller system and replicate it after 
that. How exactly can I do replication?


It may or may not help, but I don't think it likely.  You can always try it and 
see.  Certainly minimizing a smaller system will give you a faster result.  You 
can replicate any unit cell in any dimension using genconf -nbox.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] minimization and simulation problems

[politr]

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 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. 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
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  nan,  nan}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.

---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

---

"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
applicati

Re: [gmx-users] minimization and simulation problems

[politr]

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 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
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
  Box (3x3):
 Box[0]={ nan,  nan,  nan}
 Box[1]={ nan,  nan,  nan}
 Box[2]={ nan,  nan,  nan}
  Can not fix pbc.

---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

---

"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]

Re: [gmx-users] Minimization and torsion angles

[Mark Abraham]

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 am sure of this because when I run the same structure in Insight it 
is able to correct them. Both programs give very similar structures 
with the major difference being the torsion angles.)


Has this happened because Gromacs potentials do not penalize poor 
omega angles?


Peptide bonds ordinarily have improper dihedrals on them to keep them 
close to planar.


Or have I done something wrong? (I have added by .mdp file at the end 
of the mail)
Is there a way besides applying a restraint to every torsion angle to 
induce Gromacs to correct them?


EM is a local minimization method, and the result depends on the method 
and its parameters. Perhaps choosing a larger step size with 
steepest-descent algorithm will fix your issues.


Mark



Thank you in advance for you help,
Abdullah



;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  none
integrator  =  cg
nsteps  =  2000
;
;Energy minimizing stuff
;
emtol   =  2
emstep  =  0.01

nstcomm =  1
ns_type =  grid
rlist   =  1
rcoulomb=  1
rvdw=  1
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no



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Re: [gmx-users] minimization

[Justin A. Lemkul]

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 following:

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

As far as I know for succesful minimisation potential energy must be 
between -100,000 and -1,000,000.


Potential energy is dependent upon system size and the nature of the 
interactions therein.  You should not presuppose a specific value or range thereof.


-Justin


My em.mdp file as follows

integrator= steep
emstep=0.1
nsteps=1000
nstlist=10
rlist=1.0
coulombtype=pme
rcoulomb=1.0
vdw-type=cut-off
rvdw=1.0
nstenergy=10

My minimisation stops at approximately 19,000 th step.
Is my minimisation acceptable?If no, how can I correct it?

best wishes
Mustafa



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] minimization

[Justin A. Lemkul]

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?




That depends on the system and how far from the minimum it is.


And also what is the meaning of Fmax<10?

Message: Converged to machine precision, but not to the requested 
precision Fmax<10. 



Fmax corresponds to the value of the potential energy gradient.  I'd suggest 
some textbook reading here.  If you don't understand what EM is doing, you 
probably shouldn't be running it blindly without knowing what the settings are.


-Justin


Best wishes
Mustafa



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] minimization

[Justin A. Lemkul]

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 DSSP environment 
variable has to point to the actual executable, *not* simply the directory that 
contains it.  Therefore:


export DSSP=/home/m/DSSP/dssp

do_dssp I have the below error. Although the dssp exe is in 
/usr/local/bin and also I did export, computer couldn't find dssp exe file.


What is the problem? What should I do?



Probably due to incorrect environment variable settings.

-Justin


Best wishes
Mustafa


-
Select a group: 5
Selected 5: 'MainChain'
There are 90 residues in your selected group
Reading frame   0 time0.000  
Back Off! I just backed up ddt2Vei2 to ./#ddt2Vei2.1#


---
Program do_dssp, VERSION 4.5.1
Source code file: do_dssp.c, line: 521

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddt2Vei2 ddPcoaqM > 
/dev/null 2> /dev/null

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---




mustafa bilsel wrote:
 > Hi,
 > I have a problem with dssp programme.
 > I have the programme in /home/m/DSSP. When I write
 > export DSSP=/usr/local/bin
 > and then I check /usr/local/bin I couldn't see dssp.
 > How can I handle this problem. I have caheceked gromacs website
 >
 > export DSSP=/path/to/dssp
 >
 > setenv DSSP /path/to/dssp
 >
 > commands are written.
 > Could you write export DSSP=/path/to/dssp command according to me.
 >

The proper setting for the environment variable is explained in great 
detail here:


http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

Note the line "If this is not the case, you must set the DSSP environment
variable accordingly, pointing to the actual dssp executable, not just 
the PATH

to it."

 > And also I use Ubuntu 10.04, setenv is not used, if I try to install 
it, I

 > see the package not found message.
 > What should I do about it?
 >

Learn what your shell uses and apply it.  You're more than likely 
running bash,

in which case "export" is the command to use.

-Justin



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] minimization quagmire

[Mark Abraham]

- Original Message -
From: abdullah ahmed 
Date: Wednesday, September 15, 2010 21:18
Subject: [gmx-users] minimization quagmire
To: gmx 


   
---
| 

>  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 introduction 
> of two glycines in the center creates a a cavity in this hydrophobic region.
> I had expected the leucine structure to have better(lower) energy after 
> optimization, however, the opposite was true. I have run minimization in 
> vacuum and with water (water enters the cavity) and the structure with 
> glycine has better energy in both cases.




I'm a bit confused about how water can enter a cavity in the core *during* an 
EM. I presume they were actually placed in the void during solvation, before EM?





Anyway, that's not the real point. What you've observed is that once the 
structures have reached the neighbourhood of a nearby local energy minimum, the 
glycine structure is lower in energy. You haven't necessarily found the global 
minimum, or two minima that correspond to each other in any meaningful sense. 
Even if you had, there's no particular reason to expect the difference between 
these energies to correlate with the differences in the free energy of folding 
of the two proteins (or whatever). The leucine structure might be happy enough 
to fold, but have some kind of strain that is relaxed by the glycine mutations 
- but your observations (as stated) are not evidence of this, either.




Mark

 |
---



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Re: [gmx-users] minimization problem

[Mark Abraham]

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 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)

Making 1D domain decomposition 8 x 1 x 1
Steepest Descents:
   Tolerance (Fmax)   =  1.0e-05
   Number of steps=705032704

t = 0.000 ps: Water molecule starting at atom 190501 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

---
Program mdrun_d_mpi, VERSION 4.0.5
Source code file: pme.c, line: 518

Fatal error:
3 particles communicated to PME node 7 are more than a cell length out
of the domain decomposition cell of their charge group

as part of my error message. Should I still reduce the mentioned
parameters?
Regards,

Payman

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Re: [gmx-users] minimization problem

[Itamar Kass]

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 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 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 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)
Making 1D domain decomposition 8 x 1 x 1
Steepest Descents:
 Tolerance (Fmax)   =  1.0e-05
 Number of steps=705032704

t = 0.000 ps: Water molecule starting at atom 190501 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

---
Program mdrun_d_mpi, VERSION 4.0.5
Source code file: pme.c, line: 518

Fatal error:
3 particles communicated to PME node 7 are more than a cell length  
out

of the domain decomposition cell of their charge group

as part of my error message. Should I still reduce the mentioned
parameters?
Regards,

Payman

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Re: [gmx-users] minimization problem

[Paymon Pirzadeh]

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 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 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)
> > Making 1D domain decomposition 8 x 1 x 1
> > Steepest Descents:
> >   Tolerance (Fmax)   =  1.0e-05
> >   Number of steps=705032704
> >
> > t = 0.000 ps: Water molecule starting at atom 190501 can not be  
> > settled.
> > Check for bad contacts and/or reduce the timestep.
> > Wrote pdb files with previous and current coordinates
> >
> > ---
> > Program mdrun_d_mpi, VERSION 4.0.5
> > Source code file: pme.c, line: 518
> >
> > Fatal error:
> > 3 particles communicated to PME node 7 are more than a cell length out
> > of the domain decomposition cell of their charge group
> >
> > as part of my error message. Should I still reduce the mentioned
> > parameters?
> > Regards,
> >
> > Payman
> >
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Re: [gmx-users] minimization problem

[Itamar Kass]

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 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)

Making 1D domain decomposition 8 x 1 x 1
Steepest Descents:
  Tolerance (Fmax)   =  1.0e-05
  Number of steps=705032704

t = 0.000 ps: Water molecule starting at atom 190501 can not be  
settled.

Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

---
Program mdrun_d_mpi, VERSION 4.0.5
Source code file: pme.c, line: 518

Fatal error:
3 particles communicated to PME node 7 are more than a cell length out
of the domain decomposition cell of their charge group

as part of my error message. Should I still reduce the mentioned
parameters?
Regards,

Payman

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Re: [gmx-users] minimization

[Tsjerk Wassenaar]

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

2009/8/13 Morteza Khabiri :
> 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 compare the atoms of amino acids in topology file with the topolgy file
> of other proteins which did not have any problem...the oplss number for
> all atoms is the same
> but still I could not understand where is the problem
>
> thanks
>
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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Re: [gmx-users] minimization

[Tsjerk Wassenaar]

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 first, and check the output from pdb2gmx
thoroughly. Also see if you end up with each chain in its own .itp
file.

Cheers,

Tsjerk

2009/8/13 Mark Abraham :
> 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 OPLSAA forcefiled
>
> That seems intrinsically improbable, unless the oplsaa .hdb and .tdb files
> are not coping with the structure (somehow) and generating a broken starting
> configuration and/or topology. What was the final PE and maximum force from
> the gromacs forcefield EM? I suggest you look carefully at the post-pdb2gmx
> oplsaa structure for steric clashes, unsatisified valences, etc., and then
> look at the progress of the corresponding minimization. You should see
> evidence of whatever is wrong.
>
> Mark
>
>> I tried to
>> minimized structure well  by gromacs force file and the I took the
>> minimized structure from gromacs forcefield and then I tried it in OPLSAA
>> and the problem was the same as before... I also cut my structure to some
>> pieces ( which I think that it is not reasonable) but I did it but still
>> it is not workingand the interesting point is that the protein is
>> working by gromacs forcefield well without any problem but when I want to
>> use the OPLSAA force field the problem
>> start and I could not minimized my system..I also try the AMBER forcefield
>> but the AMBER also didi not work and the result was the same as OPLSAA,
>> system was exploding...when I want use all atom the problem appear and
>> I really don't know how to manage it..I already tried different coulomb
>> type algorythm and also different integrator,, different time
>> step..different emtolbut none of them working...
>>
>> I would be happy if somebody could suggest me how could I manage it with
>> all atom forcefield...
>>
>> thanks
>>
>>
>>
>>
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] minimization

[Mark Abraham]

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 OPLSAA forcefiled


That seems intrinsically improbable, unless the oplsaa .hdb and .tdb 
files are not coping with the structure (somehow) and generating a 
broken starting configuration and/or topology. What was the final PE and 
maximum force from the gromacs forcefield EM? I suggest you look 
carefully at the post-pdb2gmx oplsaa structure for steric clashes, 
unsatisified valences, etc., and then look at the progress of the 
corresponding minimization. You should see evidence of whatever is wrong.


Mark


I tried to
minimized structure well  by gromacs force file and the I took the
minimized structure from gromacs forcefield and then I tried it in OPLSAA
and the problem was the same as before... I also cut my structure to some
pieces ( which I think that it is not reasonable) but I did it but still
it is not workingand the interesting point is that the protein is
working by gromacs forcefield well without any problem but when I want to
use the OPLSAA force field the problem
start and I could not minimized my system..I also try the AMBER forcefield
but the AMBER also didi not work and the result was the same as OPLSAA,
system was exploding...when I want use all atom the problem appear and
I really don't know how to manage it..I already tried different coulomb
type algorythm and also different integrator,, different time
step..different emtolbut none of them working...

I would be happy if somebody could suggest me how could I manage it with
all atom forcefield...

thanks




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Re: [gmx-users] minimization

[Tsjerk Wassenaar]

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 :
> 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, change coulomb type ,... but they did
>> not work ..
>>
>> As MARK suggest me I try to minimize monomer separately but the monomers
>> itself also have high energy and it is not possible to minimize them...
>
> OK, so simplify further to find the problem. Minimize just one half of a
> monomer, etc. Consider writing a script to run the minimization to make this
> process fast. Remember to look at the structures to identify obvious
> problems.
>
> Mark
>
>> I change the forcefield from olps to gromacs and minimization work. I did
>> several minimization by gromacs forcefiled and then I tried to minimized
>> the system by OPLS but again the system start exploiding...
>> Is there any idea that why the minimization work by gromacs but not work
>> with opls?
>> finally I should simulate my system by opls and if I want to do it my
>> system still not minimized for OPLS
>> I will apprecite if there will be some idea for my problem
>>
>> thanks
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] minimization

[Mark Abraham]

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, change coulomb type ,... but they did
not work ..

As MARK suggest me I try to minimize monomer separately but the monomers
itself also have high energy and it is not possible to minimize them...


OK, so simplify further to find the problem. Minimize just one half of a 
monomer, etc. Consider writing a script to run the minimization to make 
this process fast. Remember to look at the structures to identify 
obvious problems.


Mark


I change the forcefield from olps to gromacs and minimization work. I did
several minimization by gromacs forcefiled and then I tried to minimized
the system by OPLS but again the system start exploiding...
Is there any idea that why the minimization work by gromacs but not work
with opls?
finally I should simulate my system by opls and if I want to do it my
system still not minimized for OPLS
I will apprecite if there will be some idea for my problem

thanks















































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Re: [gmx-users] minimization

[Mark Abraham]

On 08/07/09, 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, change coulomb type ,... but they did
> not work and still the protein at the first step of minimization
> exploding..
> is there any suggestion to get ride of from this problem???


I answered this question less than 12 hours ago. Please don't re-post.

Mark

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Re: [gmx-users] minimization

[Mark Abraham]

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, change coulomb type ,... but they did
not work and still the protein at the first step of minimization
exploding..
is there any suggestion to get ride of from this problem???


Simplify the system to reduce it to something that does work - like just 
a monomer without solvent, then work up to more complex things.


Mark
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Re: [gmx-users] minimization

[Mark Abraham]

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 suggestions for dealing with broken exploding structures here: 
http://oldwiki.gromacs.org/index.php/blowing_up


Mark
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Re: [gmx-users] minimization problem

[Mark Abraham]

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 need to understand that decane/water/decane under periodic boundary 
conditions has only one interface... the two decane segments are 
contiguous. Further, there's nothing magical about where you've placed 
that interface with respect to your initial box, since there are an 
infinite number of mathematically equivalent alternatives. The physics 
of the system and the algorithms in GROMACS will feel free to ignore 
your arbitrary choice. If you want to reconstruct a particular choice 
after a simulation, you will need to play around with editconf and/or 
trjconv.


Mark
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Re: [gmx-users] minimization problem

[Justin A. Lemkul]

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!
 


Your system is probably not centered in the box, and thus PBC is reconstructing 
it.  Use ngmx to see how Gromacs is viewing your system.


-Justin


H. Y. Xiao
 





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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] minimization problem

[David van der Spoel]

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
;   2008.9.28 10:23
;   Input file
;
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  2
nstcomm =  1
ns_type =  grid
rlist   =  0.8
coulombtype =  cut-off
rcoulomb=  1.2
vdwtype =  cut-off
rvdw=  1.2
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no
Please help me. Thanks again!
 
H. Y. Xiao
 





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--
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: [gmx-users] minimization problems

[David van der Spoel]

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 into a part, while water 
turns into two parts. I am surprised by the minimized result. Can you 
tell me the possible reasons? Thank you very much!


Periodic boundary conditions?
 
H. Y. Xiao 
 





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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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RE: [gmx-users] minimization -- bugzilla or general advice?

[Berk Hess]

> 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 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 which could cause problems due
> > to non-linearity.
> > In Gromacs 3 we had only a coordinate version of SETTLE and LINCS
> > did not work well for "triangle constraints". So to constrain the force
> > during EM
> > we needed to use only coordinates. The trick is to add c*f to the
> > coordinates,
> > somewhat analogous to constraining velocities in leap frog, and then get the
> > force without constraint components as:
> > (x+c*f - constrained(x+c*f))/c
> > I chose c as the minimization step size divided by the maximum force.
> > But there are two issues here, for large c non-linearity problems
> > and for small c float/double accuracy issues.
> > The non-linearity issue could be causing your problems.
> 
> > Although there is also another issue: water is difficult to minimize in
> > general.
> 
> 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.
> 
> I'll try and give this a shot in GROMACS 4 soon, I suppose. And I'll
> put together a bugzilla.
> 
> Thanks,
> David

I would guess other packages would use a RATTLE like constraint algorithm,
both for water and other molecules.
So this could be the source of the problem.
But please try 4.0 before submitting a bugzilla and speculating further.

Berk.


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Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 have recurring problems with minimization in
GROMACS that I've never had in other packages, even though I do
normally use water. That makes me wonder if there is a significant
difference with how this is handled in gromacs.

David
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Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 which could cause problems due
> to non-linearity.
> In Gromacs 3 we had only a coordinate version of SETTLE and LINCS
> did not work well for "triangle constraints". So to constrain the force
> during EM
> we needed to use only coordinates. The trick is to add c*f to the
> coordinates,
> somewhat analogous to constraining velocities in leap frog, and then get the
> force without constraint components as:
> (x+c*f - constrained(x+c*f))/c
> I chose c as the minimization step size divided by the maximum force.
> But there are two issues here, for large c non-linearity problems
> and for small c float/double accuracy issues.
> The non-linearity issue could be causing your problems.

> Although there is also another issue: water is difficult to minimize in
> general.

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.

I'll try and give this a shot in GROMACS 4 soon, I suppose. And I'll
put together a bugzilla.

Thanks,
David



>
>
> Berk.
>
>
> 
> Express yourself instantly with MSN Messenger! MSN Messenger
> ___
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RE: [gmx-users] minimization -- bugzilla or general advice?

[Berk Hess]

> 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,
> > 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 SETTLE.
> > This seems to improve the accuracy a lot.
> 
> I'm running without constraints. Can you explain in a little more
> detail what you mean here? c*f, where c is what? Why is this done? I
> know "to constrain the forces" but it's not clear to me what the
> incentive is.

I assume you are using a rigid water model, and thus constraints via SETTLE.

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 which could cause problems due
to non-linearity.
In Gromacs 3 we had only a coordinate version of SETTLE and LINCS
did not work well for "triangle constraints". So to constrain the force during 
EM
we needed to use only coordinates. The trick is to add c*f to the coordinates,
somewhat analogous to constraining velocities in leap frog, and then get the
force without constraint components as:
(x+c*f - constrained(x+c*f))/c
I chose c as the minimization step size divided by the maximum force.
But there are two issues here, for large c non-linearity problems
and for small c float/double accuracy issues.
The non-linearity issue could be causing your problems.

Although there is also another issue: water is difficult to minimize in general.

Berk.


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Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 SETTLE.
> This seems to improve the accuracy a lot.

I'm running without constraints. Can you explain in a little more
detail what you mean here? c*f, where c is what? Why is this done? I
know "to constrain the forces" but it's not clear to me what the
incentive is.

> Could you check if using Gromacs 4 solves your problems?

I'll check and see.

Thanks,
David

> Berk.
>
>
> 
> Express yourself instantly with MSN Messenger! MSN Messenger
> ___
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RE: [gmx-users] minimization -- bugzilla or general advice?

[Berk Hess]

> 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" 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 send in my previous e-mail holds true regardless of which
> > emstep value I use (default vs 1.0e-8).
> > 
> >>  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 default value emstep=0.01 nm or something
> >>  bigger than 1.0e-8?
> > 
> > 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
> > steps are the more accurately it should be able to find the minimum.
> > 
> David,
> 
> if you add 1+1e-8 in float at least the result is 1. Since coordinates 
> in typical systems are on the order of a few nm such a stepsize does 
> indeed not make sense, but since you tried larger stepsize as well the 
> problem is real. The stepsize is used as the maximum displacement along 
> the force vector in the steep algorithm.
> 
> I encourage you to submit a bugzilla with a few examples.

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 SETTLE.
This seems to improve the accuracy a lot.

Could you check if using Gromacs 4 solves your problems?

Berk.


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Re: [gmx-users] minimization -- bugzilla or general advice?

[David van der Spoel]

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 help. So
everything I send in my previous e-mail holds true regardless of which
emstep value I use (default vs 1.0e-8).


 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 default value emstep=0.01 nm or something
 bigger than 1.0e-8?


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
steps are the more accurately it should be able to find the minimum.


David,

if you add 1+1e-8 in float at least the result is 1. Since coordinates 
in typical systems are on the order of a few nm such a stepsize does 
indeed not make sense, but since you tried larger stepsize as well the 
problem is real. The stepsize is used as the maximum displacement along 
the force vector in the steep algorithm.


I encourage you to submit a bugzilla with a few examples.



Thanks,
David



 Best
 XAvier



 > 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 of specified size, with a
 > specified distance tolerance between atoms, to generate starting gro
 > files. I am simulating a number of variants of this peptide in various
 > mixes of the two co-solvents (one of which is water).
 >
 > The problem I am having is that, even in double precision, gromacs
 > fails to properly minimize some of the systems -- minimization using
 > any of the minimizers I've tried (including steepest descents, my
 > preference) often terminates early (i.e. after ~50 steps) even in
 > double precision, leaving really large forces on some of the atoms
 > (usually 10^10 or more). The largest forces are usually on one atom of
 > a water molecule. Hence, when I plug the minimized output into
 > equilibration, my simulations explode due to large forces.
 >
 > Small tweaks to the system can change whether minimization works
 > properly or not in some cases -- for example, switching from double
 > precision to single precision will make some systems which fail in
 > double minimize properly, as will changing cutoffs. I assume also
 > things like changing architectures will allow some systems to minimize
 > (I've seen this behavior in the past).
 >
 > The problem is, I can find no combination of settings which will allow
 > *all* of my systems to minimize properly. Inevitably some fail, and I
 > end up having to go in by hand, look at the minimization log file, see
 > which water molecule has the huge force on it, and tweak its position
 > slightly by hand in the input gro file. Typically then minimization
 > will proceed just fine.
 >
 > This brings me to my question: Are the minimization algorithms
 > truncating some of the forces at some threshold value or something?
 > That is, why does minimization often end even though forces are still
 > huge?
 >
 > Currently, I'm using steepest descents with constraints turned off,
 > double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
 > = 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
 > ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
 > and switched vdw.
 >
 > Any tips will be appreciated. Having to tweak coordinates by hand (or
 > write a script to do it) to get things to minimize isn't really a
 > satisfactory solution for me.
 >
 > I could submit a bugzilla, but I imagine what will happen if I submit
 > the cases that don't work for me is that they'll work fine for whoever
 > addresses the bugzilla and so this won't be regarded as a real
 > problem. Alternatively I could submit a whole slate of starting system
 > configurations and someone can debug just the ones that fail for them.
 >
 > Thanks,
 > David
 > ___
 > gmx-users mailing listgmx-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
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 -
 XAvier Periole - PhD

 NMR & Molecular Dynamics Group
 University of Groningen
 The Netherlands
 http://md.chem.rug.nl/~periole
 

Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 guess exactly this happens in your failing simulations: Your
>  system is stuck in a local minimum high up on the slopes of the energy
>  funnel. I guess this is just normal and happens some times. You might
>  alter the system by a little modeling (move the problematic atoms
>  slightly), or try -DFLEXIBLE, or perhaps rather increase step size.
>  Double precision minimization has proved to be more stable for me in
>  problematic cases, like straightening out a skewed average structure
>  of a trajectory.

If the system is truly in a local minimum, the force should be small,
right, since the force is by definition zero at any minimum (local or
otherwise)? I agree there may be situations in which the *energy* may
still be very unfavorable after minimization, but the forces should be
small.

I should note that I never have these problems (incomplete
minimization) with any other simulation package I use, so I strongly
suspect that the problem is something that GROMACS in particular is
doing in minimization, and *not* just a general problem with
minimizing on a high-dimensional landscape.

David

>  Regards
>
>  Christian
>
>
>
>
>  > Thanks,
>  > David
>  >
>  >
>  >>  Best
>  >>  XAvier
>  >>
>  >>
>  >>
>  >>  > 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 of specified size, with a
>  >>  > specified distance tolerance between atoms, to generate starting gro
>  >>  > files. I am simulating a number of variants of this peptide in various
>  >>  > mixes of the two co-solvents (one of which is water).
>  >>  >
>  >>  > The problem I am having is that, even in double precision, gromacs
>  >>  > fails to properly minimize some of the systems -- minimization using
>  >>  > any of the minimizers I've tried (including steepest descents, my
>  >>  > preference) often terminates early (i.e. after ~50 steps) even in
>  >>  > double precision, leaving really large forces on some of the atoms
>  >>  > (usually 10^10 or more). The largest forces are usually on one atom of
>  >>  > a water molecule. Hence, when I plug the minimized output into
>  >>  > equilibration, my simulations explode due to large forces.
>  >>  >
>  >>  > Small tweaks to the system can change whether minimization works
>  >>  > properly or not in some cases -- for example, switching from double
>  >>  > precision to single precision will make some systems which fail in
>  >>  > double minimize properly, as will changing cutoffs. I assume also
>  >>  > things like changing architectures will allow some systems to minimize
>  >>  > (I've seen this behavior in the past).
>  >>  >
>  >>  > The problem is, I can find no combination of settings which will allow
>  >>  > *all* of my systems to minimize properly. Inevitably some fail, and I
>  >>  > end up having to go in by hand, look at the minimization log file, see
>  >>  > which water molecule has the huge force on it, and tweak its position
>  >>  > slightly by hand in the input gro file. Typically then minimization
>  >>  > will proceed just fine.
>  >>  >
>  >>  > This brings me to my question: Are the minimization algorithms
>  >>  > truncating some of the forces at some threshold value or something?
>  >>  > That is, why does minimization often end even though forces are still
>  >>  > huge?
>  >>  >
>  >>  > Currently, I'm using steepest descents with constraints turned off,
>  >>  > double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
>  >>  > = 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
>  >>  > ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
>  >>  > and switched vdw.
>  >>  >
>  >>  > Any tips will be appreciated. Having to tweak coordinates by hand (or
>  >>  > write a script to do it) to get things to minimize isn't really a
>  >>  > satisfactory solution for me.
>  >>  >
>  >>  > I could submit a bugzilla, but I imagine what will happen if I submit
>  >>  > the cases that don't work for me is that they'll work fine for whoever
>  >>  > addresses the bugzilla and so this won't be regarded as a real
>  >>  > problem. Alternatively I could submit a whole slate of starting system
>  >>  > configurations and someone can debug just the ones that fail for them.
>  >>  >
>  >>  > Thanks,
>  >>  > David
>  >>  > ___
>  >>  > gmx-users mailing listgmx-users@gromacs.org
>  >>  > http://www.gromacs.org/mailman/lis

Re: [gmx-users] minimization -- bugzilla or general advice?

[Christian Burisch]

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 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 guess exactly this happens in your failing simulations: Your 
system is stuck in a local minimum high up on the slopes of the energy 
funnel. I guess this is just normal and happens some times. You might 
alter the system by a little modeling (move the problematic atoms 
slightly), or try -DFLEXIBLE, or perhaps rather increase step size. 
Double precision minimization has proved to be more stable for me in 
problematic cases, like straightening out a skewed average structure 
of a trajectory.


Regards

Christian



Thanks,
David



 Best
 XAvier



 > 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 of specified size, with a
 > specified distance tolerance between atoms, to generate starting gro
 > files. I am simulating a number of variants of this peptide in various
 > mixes of the two co-solvents (one of which is water).
 >
 > The problem I am having is that, even in double precision, gromacs
 > fails to properly minimize some of the systems -- minimization using
 > any of the minimizers I've tried (including steepest descents, my
 > preference) often terminates early (i.e. after ~50 steps) even in
 > double precision, leaving really large forces on some of the atoms
 > (usually 10^10 or more). The largest forces are usually on one atom of
 > a water molecule. Hence, when I plug the minimized output into
 > equilibration, my simulations explode due to large forces.
 >
 > Small tweaks to the system can change whether minimization works
 > properly or not in some cases -- for example, switching from double
 > precision to single precision will make some systems which fail in
 > double minimize properly, as will changing cutoffs. I assume also
 > things like changing architectures will allow some systems to minimize
 > (I've seen this behavior in the past).
 >
 > The problem is, I can find no combination of settings which will allow
 > *all* of my systems to minimize properly. Inevitably some fail, and I
 > end up having to go in by hand, look at the minimization log file, see
 > which water molecule has the huge force on it, and tweak its position
 > slightly by hand in the input gro file. Typically then minimization
 > will proceed just fine.
 >
 > This brings me to my question: Are the minimization algorithms
 > truncating some of the forces at some threshold value or something?
 > That is, why does minimization often end even though forces are still
 > huge?
 >
 > Currently, I'm using steepest descents with constraints turned off,
 > double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
 > = 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
 > ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
 > and switched vdw.
 >
 > Any tips will be appreciated. Having to tweak coordinates by hand (or
 > write a script to do it) to get things to minimize isn't really a
 > satisfactory solution for me.
 >
 > I could submit a bugzilla, but I imagine what will happen if I submit
 > the cases that don't work for me is that they'll work fine for whoever
 > addresses the bugzilla and so this won't be regarded as a real
 > problem. Alternatively I could submit a whole slate of starting system
 > configurations and someone can debug just the ones that fail for them.
 >
 > Thanks,
 > David
 > ___
 > gmx-users mailing listgmx-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]
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 -
 XAvier Periole - PhD

 NMR & Molecular Dynamics Group
 University of Groningen
 The Netherlands
 http://md.chem.rug.nl/~periole
 -
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Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 forces are still
huge, and remain so regardless of which step size I use. Any thoughts?

Thanks,
David


>  Mark
>
>
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Re: [gmx-users] minimization -- bugzilla or general advice?

[Mark Abraham]

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
steps are the more accurately it should be able to find the minimum.


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


Mark
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Re: [gmx-users] minimization -- bugzilla or general advice?

[David Mobley]

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 send in my previous e-mail holds true regardless of which
emstep value I use (default vs 1.0e-8).

>  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 default value emstep=0.01 nm or something
>  bigger than 1.0e-8?

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
steps are the more accurately it should be able to find the minimum.

Thanks,
David


>  Best
>  XAvier
>
>
>
>  > 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 of specified size, with a
>  > specified distance tolerance between atoms, to generate starting gro
>  > files. I am simulating a number of variants of this peptide in various
>  > mixes of the two co-solvents (one of which is water).
>  >
>  > The problem I am having is that, even in double precision, gromacs
>  > fails to properly minimize some of the systems -- minimization using
>  > any of the minimizers I've tried (including steepest descents, my
>  > preference) often terminates early (i.e. after ~50 steps) even in
>  > double precision, leaving really large forces on some of the atoms
>  > (usually 10^10 or more). The largest forces are usually on one atom of
>  > a water molecule. Hence, when I plug the minimized output into
>  > equilibration, my simulations explode due to large forces.
>  >
>  > Small tweaks to the system can change whether minimization works
>  > properly or not in some cases -- for example, switching from double
>  > precision to single precision will make some systems which fail in
>  > double minimize properly, as will changing cutoffs. I assume also
>  > things like changing architectures will allow some systems to minimize
>  > (I've seen this behavior in the past).
>  >
>  > The problem is, I can find no combination of settings which will allow
>  > *all* of my systems to minimize properly. Inevitably some fail, and I
>  > end up having to go in by hand, look at the minimization log file, see
>  > which water molecule has the huge force on it, and tweak its position
>  > slightly by hand in the input gro file. Typically then minimization
>  > will proceed just fine.
>  >
>  > This brings me to my question: Are the minimization algorithms
>  > truncating some of the forces at some threshold value or something?
>  > That is, why does minimization often end even though forces are still
>  > huge?
>  >
>  > Currently, I'm using steepest descents with constraints turned off,
>  > double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
>  > = 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
>  > ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
>  > and switched vdw.
>  >
>  > Any tips will be appreciated. Having to tweak coordinates by hand (or
>  > write a script to do it) to get things to minimize isn't really a
>  > satisfactory solution for me.
>  >
>  > I could submit a bugzilla, but I imagine what will happen if I submit
>  > the cases that don't work for me is that they'll work fine for whoever
>  > addresses the bugzilla and so this won't be regarded as a real
>  > problem. Alternatively I could submit a whole slate of starting system
>  > configurations and someone can debug just the ones that fail for them.
>  >
>  > Thanks,
>  > David
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>  > Please search the archive at http://www.gromacs.org/search before posting!
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>
>  -
>  XAvier Periole - PhD
>
>  NMR & Molecular Dynamics Group
>  University of Groningen
>  The Netherlands
>  http://md.chem.rug.nl/~periole
>  -
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Re: [gmx-users] minimization -- bugzilla or general advice?

[Xavier Periole]

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 default value emstep=0.01 nm or something
bigger than 1.0e-8?

Best
XAvier


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 of specified size, with a
specified distance tolerance between atoms, to generate starting gro
files. I am simulating a number of variants of this peptide in various
mixes of the two co-solvents (one of which is water).

The problem I am having is that, even in double precision, gromacs
fails to properly minimize some of the systems -- minimization using
any of the minimizers I've tried (including steepest descents, my
preference) often terminates early (i.e. after ~50 steps) even in
double precision, leaving really large forces on some of the atoms
(usually 10^10 or more). The largest forces are usually on one atom of
a water molecule. Hence, when I plug the minimized output into
equilibration, my simulations explode due to large forces.

Small tweaks to the system can change whether minimization works
properly or not in some cases -- for example, switching from double
precision to single precision will make some systems which fail in
double minimize properly, as will changing cutoffs. I assume also
things like changing architectures will allow some systems to minimize
(I've seen this behavior in the past).

The problem is, I can find no combination of settings which will allow
*all* of my systems to minimize properly. Inevitably some fail, and I
end up having to go in by hand, look at the minimization log file, see
which water molecule has the huge force on it, and tweak its position
slightly by hand in the input gro file. Typically then minimization
will proceed just fine.

This brings me to my question: Are the minimization algorithms
truncating some of the forces at some threshold value or something?
That is, why does minimization often end even though forces are still
huge?

Currently, I'm using steepest descents with constraints turned off,
double precision, and emstep = 1.0e-8. I'm using Gromacs 3.3.2, rlist
= 0.9 = rcoulomb, rvdw-switch = 0.75 and rvdw = 0.8, pme_order 4,
ewald_rtol = 1e-04, and fourierspacing = 0.12, DispCorr = AllEnerPres,
and switched vdw.

Any tips will be appreciated. Having to tweak coordinates by hand (or
write a script to do it) to get things to minimize isn't really a
satisfactory solution for me.

I could submit a bugzilla, but I imagine what will happen if I submit
the cases that don't work for me is that they'll work fine for whoever
addresses the bugzilla and so this won't be regarded as a real
problem. Alternatively I could submit a whole slate of starting system
configurations and someone can debug just the ones that fail for them.

Thanks,
David
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-
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-
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Re: [gmx-users] Minimization of a box of capped tryptophan (trp)

[David van der Spoel]

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 with genbox 
command. I wanted the box to have a total of 200 capped trp molecules. In this 
respect, I used -maxsol 200 option. However, the resultant system had only 11 
capped trp molecules.

What may be the problem?


box too small?

use genconf -nbox 8 5 5 or something like that


Thanks

Oz.


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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] Minimization Issue - membrane inverted and system copied

[Arneh Babakhani]

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 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 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 of the system.  (Yes, i have my images setting in VMD
set for just the self structure).


What's going on here?  My structure, topology and mdp files are all
correct (I successfully executed previous minimizations with them).  I'm
sure it's something really obvious, by I can't figure it out.  Would
appreciate any help.


Regards,


Arneh



; VARIOUS PREPROCESSING OPTIONS =
title=
cpp  = /usr/bin/cpp
include  =
define   = -DFLEX_SPC

; RUN CONTROL PARAMETERS =
integrator   = steep
; start time and timestep in ps =
tinit= 0
dt   = 0.002
nsteps   = 5000
; 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 motion removal =
comm-grps=

; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp  = 300
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells =
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep   = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep   = 1000

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 100
nstvout  = 100
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file =
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or no =
pbc  = xyz
; nblist cut-off =
rlist= 1
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths=
rvdw-switch  = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-5
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
Tcoupl   = no
; Groups to couple separately =
tc-grps  =
; Time constant (ps) and reference temperature (K) =
tau-t=
ref-t=
; Pressure coupling  =
Pcoupl   = no
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p= 1
compressibility  =
ref-p=

; SIMULATED ANNEALING CONTROL =
annealing= no
; Time at which temperature should be zero (ps) =
zero-temp_time   = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = no
gen-temp = 300
gen-seed = 173529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint-algorithm

Re: [gmx-users] Minimization Issue - membrane inverted and system copied

[Tsjerk Wassenaar]

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 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 of the system.  (Yes, i have my images setting in VMD
set for just the self structure).


What's going on here?  My structure, topology and mdp files are all
correct (I successfully executed previous minimizations with them).  I'm
sure it's something really obvious, by I can't figure it out.  Would
appreciate any help.


Regards,


Arneh



; VARIOUS PREPROCESSING OPTIONS =
title=
cpp  = /usr/bin/cpp
include  =
define   = -DFLEX_SPC

; RUN CONTROL PARAMETERS =
integrator   = steep
; start time and timestep in ps =
tinit= 0
dt   = 0.002
nsteps   = 5000
; 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 motion removal =
comm-grps=

; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp  = 300
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells =
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep   = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep   = 1000

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 100
nstvout  = 100
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 100
nstenergy= 100
; Output frequency and precision for xtc file =
nstxtcout= 0
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or no =
pbc  = xyz
; nblist cut-off =
rlist= 1
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths=
rvdw-switch  = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-5
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
Tcoupl   = no
; Groups to couple separately =
tc-grps  =
; Time constant (ps) and reference temperature (K) =
tau-t=
ref-t=
; Pressure coupling  =
Pcoupl   = no
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p= 1
compressibility  =
ref-p=

; SIMULATED ANNEALING CONTROL =
annealing= no
; Time at which temperature should be zero (ps) =
zero-temp_time   = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = no
gen-temp = 300
gen-seed = 173529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Use successive overrelaxation to reduce the number of shake iterations =
Shake-SO