Re: [gmx-users] question about energy minimization

[Justin A. Lemkul]

On 7/5/12 10:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I want to minimize the energy of my structure.
I use the following mdp file:

define  = -DPOSRES
integrator  = steep
emtol   = 10
nsteps  = 5000
nstenergy   = 1
energygrps  = System
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
rlist   = 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
pbc = xyz

But it nevers runs till the end. It allways stops before the end and I get
no pdb file. When I use nsteps = 2000 there is no problem and I receive a
pdb file but it says that there were not enough steps to get under a
specific force value.

My question is: is there a possibility to make the minimization run
longer? Can I set a parameter that makes it run longer?



Set nsteps to either a very high value or to -1 (which says run infinitely 
long).  Note that several factors are working against you here, including the 
use of position restraints.  These disfavor the motion of whatever the 
restrained atoms are, which can impede energy minimization.  Also, assuming 
you're using single-precision Gromacs, an emtol of 10 is very low and unlikely 
to be achievable, especially using a single run of steepest descent EM.


-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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[gmx-users] question about energy minimization

[reisingere]

Hi everybody,
I want to minimize the energy of my structure.
I use the following mdp file:

define  = -DPOSRES
integrator  = steep
emtol   = 10
nsteps  = 5000
nstenergy   = 1
energygrps  = System
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
rlist   = 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
pbc = xyz

But it nevers runs till the end. It allways stops before the end and I get
no pdb file. When I use nsteps = 2000 there is no problem and I receive a
pdb file but it says that there were not enough steps to get under a
specific force value.

My question is: is there a possibility to make the minimization run
longer? Can I set a parameter that makes it run longer?

Thank you,
Eva

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Re: [gmx-users] question about energy minimization

[Mark Abraham]

On 4/07/2012 5:46 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,

is there a possibility to define an energy value and when the change of
the energy between two steps during the minimization is lower than this
value the minimization is finished?



If it's in manual 7.3.5, you can do it.

Mark
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[gmx-users] question about energy minimization

[reisingere]

Hi everybody,

is there a possibility to define an energy value and when the change of
the energy between two steps during the minimization is lower than this
value the minimization is finished?

Thank you,
Eva

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Re: [gmx-users] question about energy minimization

[Justin A. Lemkul]

Amit Choubey wrote:

Hi Omer,

My question was to how to avoid the "diffusion" of molecules out of the 
box during energy minimization and MD  run? I think what you suggested 
here will just change the present trajectory into a new by using the pbc 
condition.




There is no "outside" in a periodic system.  EM should not be causing huge 
changes to your system; if particles are flying around chaotically, your system 
is probably not stable.


But i am wondering shouldnt this be done in MD calculation itself. It 
seems me to me that physics will be significantly different if i dont 
put the particles which go out of the box, back into the box. In that 
way the box will keep on expanding as i increase my simulation time and 
the calculated equilibirium properties wont be very meaningful and will 
fluctuate more than they really should.




If you have inserted molecules into the system by force (if I recall the 
original post), you should expect the system to expand.  Omer's suggestion was 
post-processing for proper visualization; periodicity is accounted for in the MD 
calculation.


The box will continue to expand until it reaches equilibrium, if possible. 
After you obtain a stable box, you may be able to collect meaningful data.


-Justin

By the way i am talking about long chain lipid molecules here and i am 
using an all bond constraint.


Amit



On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch > wrote:


Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help
printed. Omer.

 



I actually didnt realize this until i did a long simulation
after which the trajectories of some of the atoms looked way out
of the box dimensions. The co-ordinates of many atoms didnt lie
in the box range. Although the output file contained the same
box dimensions as I started with. Could someone help me in
understanding what happened?



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] question about energy minimization

[Amit Choubey]

Hi Omer,

My question was to how to avoid the "diffusion" of molecules out of the box
during energy minimization and MD  run? I think what you suggested here will
just change the present trajectory into a new by using the pbc condition.

But i am wondering shouldnt this be done in MD calculation itself. It seems
me to me that physics will be significantly different if i dont put the
particles which go out of the box, back into the box. In that way the box
will keep on expanding as i increase my simulation time and the calculated
equilibirium properties wont be very meaningful and will fluctuate more than
they really should.

By the way i am talking about long chain lipid molecules here and i am using
an all bond constraint.

Amit



On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch  wrote:

> Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.
> Omer.
>
>
>>
>> I actually didnt realize this until i did a long simulation after which
>> the trajectories of some of the atoms looked way out of the box dimensions.
>> The co-ordinates of many atoms didnt lie in the box range. Although the
>> output file contained the same box dimensions as I started with. Could
>> someone help me in understanding what happened?
>>
>>
>
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Re: [gmx-users] question about energy minimization

[Omer Markovitch]

Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.
Omer.


>
> I actually didnt realize this until i did a long simulation after which the
> trajectories of some of the atoms looked way out of the box dimensions. The
> co-ordinates of many atoms didnt lie in the box range. Although the output
> file contained the same box dimensions as I started with. Could someone help
> me in understanding what happened?
>
>
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[gmx-users] question about energy minimization

[Amit Choubey]

Hi everyone,
I recently was doing a simulation where i had inserted water into the system
forcefully( using -ci -nmol option of the genbox). I didnt change the box
dimensions after the insertion of the extra molecules. Then i did energy
minimization on the system and somehow it moved the atoms out of the box
(some co-ordinates became negative and some became more than the box size).
I did not want the program to do this i would have rather removed some of
the molecules. Is there a way to control this? Interestingly, the energy
minimization log didnt show any of the above changes, it also didnt change
the box size in its output gro file?

I actually didnt realize this until i did a long simulation after which the
trajectories of some of the atoms looked way out of the box dimensions. The
co-ordinates of many atoms didnt lie in the box range. Although the output
file contained the same box dimensions as I started with. Could someone help
me in understanding what happened?

Thank you,
Amit Choubey
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