RE: [gmx-users] Problems with umbrella sampling

[Berk Hess]

Hi,

I think you want pull_dim = Y Y Y
and for umbrella sampling you need pull=umbrella

Berk

Date: Thu, 11 Mar 2010 17:37:34 -0800
From: jrcase...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Problems with umbrella sampling

Hello,

I am interested in creating a PMF for Na+ and I- in the presence of THF 
(tetrahydrofuran).  I am having a couple of issues though.

First, I have followed the umbrella sampling tutorial on the gromacs website 
very careful, and I think I am doing everything right.  I minimized the energy 
of my system, did a short equilibrium run, and then pulled Na+ and I- away from 
each other at a specified rate.  This generated starting configurations, which 
I used in my umbrella sampling (see attached file ).  Once I had many umbrella 
sampling windows, I used g_wham to recombine them.  First I looked at the 
histograms.  I have good overlap, but I notice some very odd features:


1)  I see substantial shifting towards lower distances between Na+ and I-, no 
matter what the initial distances they start separated at.  I would expect this 
if I am near an equilibrium distance, but I see it for all distances.

2)  My original pull simulation (where I specificed a rate) started Na+ and I- 
0.27 nm apart.  All of my starting configurations are 0.27 nm apart or further. 
 If I run some of the umbrella sampling simulations at 0.27 nm, I see that the 
Na+ and I- reach distances as low as 0.03 nm!  This is completely unphysical 
(both in that my spring constant is strong enough to supposedly prevent such 
large drifts and because the two molecules should not want to be on top of each 
other).  


To check these issues out, I tried to do a couple of things:

I want to pull the Na+ and I- closer together than 0.27 nm, and see if I get 
the steep increase in energy, like I expect.  I am having problems with this 
part though.  I have not been able to pull my molecules closer together when 
starting at 0.27 nm, so I tried to start them closer together and then pull 
them apart by using the following in my .mdp file:


pull = constraint
pull_geometry = distance
pull_dim = Y N N
pull_start = yes
pull_ngroups = 1
pull_group0 = Na+
pull_group1 = I-
pull_vec1 = 1 0 0
pull_init1 = 0.1 (I think this means that I- starts 0.1 nm away from Na+?)

pull_rate1 = 0.005

When I do this, I still get my molecules being pulled apart from 0.27 nm to 
further distances apart.  I also tried using no pull_init1, but using pull_vec1 
= -1 0 0, but that didn't work either.  Whenever I tried to use pull_geometry = 
position, I got segmentation faults...


Has anyone else experienced these issues?  Is there a way to bring Na+ and I- 
closer?  I have checked older posts, but the suggestions I keep seeing (i.e. 
use pull_init1) aren't working for me.

Thank you!

Jenny
  
_
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[gmx-users] Problems with umbrella sampling

[Jennifer Casey]

Hello,

I am interested in creating a PMF for Na+ and I- in the presence of THF
(tetrahydrofuran).  I am having a couple of issues though.

First, I have followed the umbrella sampling tutorial on the gromacs website
very careful, and I think I am doing everything right.  I minimized the
energy of my system, did a short equilibrium run, and then pulled Na+ and I-
away from each other at a specified rate.  This generated starting
configurations, which I used in my umbrella sampling (see attached file ).
Once I had many umbrella sampling windows, I used g_wham to recombine them.
First I looked at the histograms.  I have good overlap, but I notice some
very odd features:

1)  I see substantial shifting towards lower distances between Na+ and I-,
no matter what the initial distances they start separated at.  I would
expect this if I am near an equilibrium distance, but I see it for all
distances.
2)  My original pull simulation (where I specificed a rate) started Na+ and
I- 0.27 nm apart.  All of my starting configurations are 0.27 nm apart or
further.  If I run some of the umbrella sampling simulations at 0.27 nm, I
see that the Na+ and I- reach distances as low as 0.03 nm!  This is
completely unphysical (both in that my spring constant is strong enough to
supposedly prevent such large drifts and because the two molecules should
not want to be on top of each other).

To check these issues out, I tried to do a couple of things:

I want to pull the Na+ and I- closer together than 0.27 nm, and see if I get
the steep increase in energy, like I expect.  I am having problems with this
part though.  I have not been able to pull my molecules closer together when
starting at 0.27 nm, so I tried to start them closer together and then pull
them apart by using the following in my .mdp file:

pull = constraint
pull_geometry = distance
pull_dim = Y N N
pull_start = yes
pull_ngroups = 1
pull_group0 = Na+
pull_group1 = I-
pull_vec1 = 1 0 0
pull_init1 = 0.1 (I think this means that I- starts 0.1 nm away from Na+?)
pull_rate1 = 0.005

When I do this, I still get my molecules being pulled apart from 0.27 nm to
further distances apart.  I also tried using no pull_init1, but using
pull_vec1 = -1 0 0, but that didn't work either.  Whenever I tried to use
pull_geometry = position, I got segmentation faults...

Has anyone else experienced these issues?  Is there a way to bring Na+ and
I- closer?  I have checked older posts, but the suggestions I keep seeing
(i.e. use pull_init1) aren't working for me.

Thank you!
Jenny


thfrun_us.mdp
Description: Binary data
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Re: [gmx-users] Problems with umbrella sampling

[Justin A. Lemkul]

Amir Marcovitz wrote:

Thanks Justin,
 
it seems to help, i have another general question that you might help me 
with:
 
should i define the distances for the umbrella sampling run in some file 
and then run it?(i saw something about  *.ppa file but couldn't find any 
further instructions in the mannual..)

will this file apply for the WHAM analysis after the run?
 


All settings are defined in the .mdp file (see, i.e. pull_start and pull_init). 
 Using .ppa files is obsolete (version 3.x and before).  The WHAM analysis 
later reads these distances from the .tpr files passed to g_wham.


There are many discussions (some quite recent) in the list archive about proper 
settings.  I suggest you have a look at the manual and then go searching.


-Justin


thanks,
Amir

On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul > wrote:




Amir Marcovitz wrote:

Hi,
 my system is constructed of 2 parallel plates in a box with
solvent. each plate is made of 36 atoms which are positively
charged on one of them (SRP) and negatively charged on the other
plate (SRN).
 i want to perform a simulation with umbrella sampling between
the 2 so i defined the pulling section parameters in the .mdp
parameter file as following:
 ; COM PULLING ; Pull type: no, umbrella, constraint or
constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 2
; Group name, weight (default all 1), vector, init, rate
(nm/ps), kJ/(mol*nm^2)
pull_group0  = SRP
pull_weights0= 1
pull_pbcatom0= 0
pull_group1  = SRN
pull_weights1= 1
pull_pbcatom1= 0
pull_vec1= 0.0 1.0 0.0
pull_init1   = 1.5
pull_rate1   = 0
pull_k1  = 1
pull_kB1 = 0
 when proccesing the file with grompp i get the following error:
 *Fatal error:
Number of weights (1) for pull group 0 'SRP' does not match the
number of atoms (36)*
 is someone recognizing my mistake?


Please refer to the manual (manual.gromacs.org
 is quite handy), you will find:

"Optional relative weights which are multiplied with the masses of
the atoms to give the total weight for the COM. The number should be
0, meaning all 1, or the number of atoms in the pull group."

I also think your value for pull_ngroup is wrong.  It appears you
are pulling SRN with respect to SRP, so you only have one pull
group, not two.

-Justin

does someone has an experience with umbrella sampling in GROMACS?
 thanks'
amir
*
*


-- 



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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--


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] Problems with umbrella sampling

[Amir Marcovitz]

Thanks Justin,

it seems to help, i have another general question that you might help me
with:

should i define the distances for the umbrella sampling run in some file and
then run it?(i saw something about  *.ppa file but couldn't find any further
instructions in the mannual..)
will this file apply for the WHAM analysis after the run?

thanks,
Amir

On Mon, Dec 28, 2009 at 6:14 PM, Justin A. Lemkul  wrote:

>
>
> Amir Marcovitz wrote:
>
>> Hi,
>>  my system is constructed of 2 parallel plates in a box with solvent. each
>> plate is made of 36 atoms which are positively charged on one of them (SRP)
>> and negatively charged on the other plate (SRN).
>>  i want to perform a simulation with umbrella sampling between the 2 so i
>> defined the pulling section parameters in the .mdp parameter file as
>> following:
>>  ; COM PULLING ; Pull type: no, umbrella, constraint or
>> constant_force
>> pull = umbrella
>> ; Pull geometry: distance, direction, cylinder or position
>> pull_geometry= distance
>> ; Select components for the pull vector. default: Y Y Y
>> pull_dim = Y Y Y
>> ; Cylinder radius for dynamic reaction force groups (nm)
>> pull_r1  = 1
>> ; Switch from r1 to r0 in case of dynamic reaction force
>> pull_r0  = 1.5
>> pull_constr_tol  = 1e-06
>> pull_start   = no
>> pull_nstxout = 10
>> pull_nstfout = 1
>> ; Number of pull groups
>> pull_ngroups = 2
>> ; Group name, weight (default all 1), vector, init, rate (nm/ps),
>> kJ/(mol*nm^2)
>> pull_group0  = SRP
>> pull_weights0= 1
>> pull_pbcatom0= 0
>> pull_group1  = SRN
>> pull_weights1= 1
>> pull_pbcatom1= 0
>> pull_vec1= 0.0 1.0 0.0
>> pull_init1   = 1.5
>> pull_rate1   = 0
>> pull_k1  = 1
>> pull_kB1 = 0
>>  when proccesing the file with grompp i get the following error:
>>  *Fatal error:
>> Number of weights (1) for pull group 0 'SRP' does not match the number of
>> atoms (36)*
>>  is someone recognizing my mistake?
>>
>
> Please refer to the manual (manual.gromacs.org is quite handy), you will
> find:
>
> "Optional relative weights which are multiplied with the masses of the
> atoms to give the total weight for the COM. The number should be 0, meaning
> all 1, or the number of atoms in the pull group."
>
> I also think your value for pull_ngroup is wrong.  It appears you are
> pulling SRN with respect to SRP, so you only have one pull group, not two.
>
> -Justin
>
>  does someone has an experience with umbrella sampling in GROMACS?
>>  thanks'
>> amir
>> *
>> *
>>
>>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] Problems with umbrella sampling

[Justin A. Lemkul]

Amir Marcovitz wrote:

Hi,
 
my system is constructed of 2 parallel plates in a box with solvent. 
each plate is made of 36 atoms which are positively charged on one of 
them (SRP) and negatively charged on the other plate (SRN).
 
i want to perform a simulation with umbrella sampling between the 2 so i 
defined the pulling section parameters in the .mdp parameter file as 
following:
 
; COM PULLING 
; Pull type: no, umbrella, constraint or constant_force

pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 2
; Group name, weight (default all 1), vector, init, rate (nm/ps), 
kJ/(mol*nm^2)

pull_group0  = SRP
pull_weights0= 1
pull_pbcatom0= 0
pull_group1  = SRN
pull_weights1= 1
pull_pbcatom1= 0
pull_vec1= 0.0 1.0 0.0
pull_init1   = 1.5
pull_rate1   = 0
pull_k1  = 1
pull_kB1 = 0
 
when proccesing the file with grompp i get the following error:
 
*Fatal error:
Number of weights (1) for pull group 0 'SRP' does not match the number 
of atoms (36)*
 
is someone recognizing my mistake?


Please refer to the manual (manual.gromacs.org is quite handy), you will find:

"Optional relative weights which are multiplied with the masses of the atoms to 
give the total weight for the COM. The number should be 0, meaning all 1, or the 
number of atoms in the pull group."


I also think your value for pull_ngroup is wrong.  It appears you are pulling 
SRN with respect to SRP, so you only have one pull group, not two.


-Justin


does someone has an experience with umbrella sampling in GROMACS?
 
thanks'

amir
*
*



--


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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[gmx-users] Problems with umbrella sampling

[Amir Marcovitz]

Hi,

my system is constructed of 2 parallel plates in a box with solvent. each
plate is made of 36 atoms which are positively charged on one of them (SRP)
and negatively charged on the other plate (SRN).

i want to perform a simulation with umbrella sampling between the 2 so i
defined the pulling section parameters in the .mdp parameter file as
following:

; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = Y Y Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1.5
pull_constr_tol  = 1e-06
pull_start   = no
pull_nstxout = 10
pull_nstfout = 1
; Number of pull groups
pull_ngroups = 2
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0  = SRP
pull_weights0= 1
pull_pbcatom0= 0
pull_group1  = SRN
pull_weights1= 1
pull_pbcatom1= 0
pull_vec1= 0.0 1.0 0.0
pull_init1   = 1.5
pull_rate1   = 0
pull_k1  = 1
pull_kB1 = 0

when proccesing the file with grompp i get the following error:

*Fatal error:
Number of weights (1) for pull group 0 'SRP' does not match the number of
atoms (36)*

is someone recognizing my mistake?
does someone has an experience with umbrella sampling in GROMACS?

thanks'
amir
*
*
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