Re: [gmx-users] Umbrella sampling - regd

2013-01-01 Thread ramesh cheerla 
Dear Justin,

Thank you very much for your quick reply.

Regards,
Ramesh.



On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul  wrote:

>
>
> On 1/1/13 11:48 PM, ramesh cheerla wrote:
>
>> Dear Gromacs users,
>>
>>   I am performing  umbrella sampling
>> simulations by selecting configurations with spacing window of  0.02nm
>> from
>> pulling simulations with the following options in .mdp file to get PMF
>> along a axis for permeation of ion through a channel.
>>
>> ; Pull code
>> pull= umbrella
>> pull_geometry   = position  ; simple distance increase
>> pull_dim   = N Y N
>> pull_vec1= 0 -1 0
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_ngroups= 1
>> pull_group0 = FIXEDATOM
>> pull_group1 = SMDATOM
>> pull_rate1  = 0.0 ; 0.01 nm per ps = 10 nm per ns
>> pull_k1 = 2000  ; kJ mol^-1 nm^-2
>> pull_init1  = 0
>>
>> And   am using g_wham to get PMF, while using g_wham,  am getting the
>> warnings like :
>> WARNING, no data point in bin 139 (z=-0.492557) !
>> You may not get a reasonable profile. Check your histograms!
>> Warning, poor sampling bin 193 (z=-0.364322). Check your histograms!
>> Warning, poor sampling bin 194 (z=-0.361947). Check your histograms!
>> Warning, poor sampling bin 195 (z=-0.359572). Check your histograms!
>> Warning, poor sampling bin 196 (z=-0.357197). Check your histograms!
>> Warning, poor sampling bin 197 (z=-0.354823). Check your histograms!
>> Warning, poor sampling bin 198 (z=-0.352448). Check your histograms!
>> Warning, poor sampling bin 199 (z=-0.350073). Check your histograms!
>> Initialized rapid wham stuff (contrib tolerance 6.7e-08)
>> Evaluating only 2115 of 3000 expressions.
>> I have checked my histograms and PMF profile, by doing so I have
>> understood
>> that histograms overlapping is restricted to only some regions and there
>> is
>> no histograms at all in some regions i.e severe sampling problems at
>> barrier regions.  here I am sending the link that containing PMF profile
>> that I have obtained,  http://researchweb.iiit.ac.in/**
>> ~bipin.singh/pmf.jpg 
>>
>> Can anybody tell me how can I get proper sampling at barrier regions is
>> there any efficient way to do this, how about meta dynamics with suitable
>> CV (collective variable) ? .
>>
>>
>>
> Use a stronger force constant in these barrier regions to restrict the
> movement along the reaction coordinate.
>
> -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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] Umbrella sampling - regd

2013-01-01 Thread Justin Lemkul 



On 1/1/13 11:48 PM, ramesh cheerla wrote:

Dear Gromacs users,

  I am performing  umbrella sampling
simulations by selecting configurations with spacing window of  0.02nm from
pulling simulations with the following options in .mdp file to get PMF
along a axis for permeation of ion through a channel.

; Pull code
pull= umbrella
pull_geometry   = position  ; simple distance increase
pull_dim   = N Y N
pull_vec1= 0 -1 0
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = FIXEDATOM
pull_group1 = SMDATOM
pull_rate1  = 0.0 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 2000  ; kJ mol^-1 nm^-2
pull_init1  = 0

And   am using g_wham to get PMF, while using g_wham,  am getting the
warnings like :
WARNING, no data point in bin 139 (z=-0.492557) !
You may not get a reasonable profile. Check your histograms!
Warning, poor sampling bin 193 (z=-0.364322). Check your histograms!
Warning, poor sampling bin 194 (z=-0.361947). Check your histograms!
Warning, poor sampling bin 195 (z=-0.359572). Check your histograms!
Warning, poor sampling bin 196 (z=-0.357197). Check your histograms!
Warning, poor sampling bin 197 (z=-0.354823). Check your histograms!
Warning, poor sampling bin 198 (z=-0.352448). Check your histograms!
Warning, poor sampling bin 199 (z=-0.350073). Check your histograms!
Initialized rapid wham stuff (contrib tolerance 6.7e-08)
Evaluating only 2115 of 3000 expressions.
I have checked my histograms and PMF profile, by doing so I have understood
that histograms overlapping is restricted to only some regions and there is
no histograms at all in some regions i.e severe sampling problems at
barrier regions.  here I am sending the link that containing PMF profile
that I have obtained,  http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg

Can anybody tell me how can I get proper sampling at barrier regions is
there any efficient way to do this, how about meta dynamics with suitable
CV (collective variable) ? .




Use a stronger force constant in these barrier regions to restrict the movement 
along the reaction coordinate.


-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] Umbrella sampling - regd

2012-11-26 Thread ramesh cheerla 
Dear Justin,

I am very thankful to you for your reply, you are correct, I have plotted
the histo.xvg file in wrong manner. After plotting histograms in correct
manner I have realized that my sampling is very poor as histograms and
there overlapping is restricted to some regions only,  no histograms in
some areas along reaction co-ordinate.
I am not sure whether this lack of  sampling is due to  inappropriate
selection of pulled configurations or  inappropriate pull geometry.
However I will try as per your suggestion and get back to you.

Thank you,

Regards,
Ramesh.



On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul  wrote:

>
>
> On 11/26/12 1:03 AM, ramesh cheerla wrote:
>
>> Dear Gromacs users,
>>
>>
>>   I am calculating  PMF for the ion permeation through a tunnel, using
>> umbrella sampling. In my system I have some binding sites with ions, I
>> have
>> removed some ions from binding sites before pulling and In pulling
>> simulations have pullaed pulled the adjacent ions to the vacant binding
>> site (tunnel is aligned along  Y- axis).
>> for this I have used the following options in .mdp file.
>> ; Pull code
>> pull= umbrella
>> pull_geometry   = distance
>> pull_dim= N Y N
>> pull_start  = yes
>> pull_ngroups= 1
>> pull_group0 = REFA
>> pull_rate1  = 0.01
>> pull_k1 = 3000  ; kJ mol^-1 nm^-2
>>
>> Here  pull_group0 = REFA is the ion at another binding site and
>> pull_group1 = ATBP  is the atom  that I am pulling to the vacant site.
>> In next step I have performed umbrella sampling simulations to the
>> selected
>> configurations using the following options :
>> ; Pull code
>> pull= umbrella
>> pull_geometry   = distance  ; simple distance increase
>> pull_dim= N Y N
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_ngroups= 1
>> pull_group0 = REFA
>> pull_group1 = ATBP
>> pull_init1  = 0
>> pull_rate1  = 0.0  ; 0.01 nm per ps = 10 nm per ns
>> pull_k1 = 3000  ; kJ mol^-1 nm^-2
>> pull_nstxout= 100
>> pull_nstfout= 100
>> After that I have constructed PMF profile using Gromacs tool "g_wham",
>> while using g_wham I am getting the following warnings,
>> "WARNING, no data point in bin 34 (z=0.889382) !
>> You may not get a reasonable profile. Check your histograms!"
>> I have checked my histograms instead of one histogram for each
>> configuration with perfect overlapping, I am getting only one histogram.
>>
>
> You're probably just plotting the file wrong.
>
> xmgrace -nxy histo.xvg
>
>
>  Here I am sending the link that containing PMF profile and histogram that
>> have obtained.
>> http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpg
>> http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpg
>>
>>
> The PMF suggests massive undersampling (or complete lack of sampling) in
> several areas.
>
>
>  the weired thing that I have observed in my pulling simulations is that I
>> have expected motion of ion in positive Y-direction for my pull parameters
>> but it is moving in negative Y- direction.
>>   Can anybody please suggest me a solution for this,  Am I following
>> correct
>> protocol to get PMF of my system, is there any better method that suits
>> for
>> my system.
>>
>>
> If you are trying to see a complete translocation of an ion through a
> channel, the "distance" geometry is inappropriate, as it does not deal
> correctly with the change of sign for the vector between the reference and
> pulled group, IIRC.  Try "position" geometry and associated settings.
>
> -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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Umbrella sampling - regd

2012-11-26 Thread Justin Lemkul 



On 11/26/12 1:03 AM, ramesh cheerla wrote:

Dear Gromacs users,


  I am calculating  PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations have pullaed pulled the adjacent ions to the vacant binding
site (tunnel is aligned along  Y- axis).
for this I have used the following options in .mdp file.
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N Y N
pull_start  = yes
pull_ngroups= 1
pull_group0 = REFA
pull_rate1  = 0.01
pull_k1 = 3000  ; kJ mol^-1 nm^-2

Here  pull_group0 = REFA is the ion at another binding site and
pull_group1 = ATBP  is the atom  that I am pulling to the vacant site.
In next step I have performed umbrella sampling simulations to the selected
configurations using the following options :
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N Y N
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = REFA
pull_group1 = ATBP
pull_init1  = 0
pull_rate1  = 0.0  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 3000  ; kJ mol^-1 nm^-2
pull_nstxout= 100
pull_nstfout= 100
After that I have constructed PMF profile using Gromacs tool "g_wham",
while using g_wham I am getting the following warnings,
"WARNING, no data point in bin 34 (z=0.889382) !
You may not get a reasonable profile. Check your histograms!"
I have checked my histograms instead of one histogram for each
configuration with perfect overlapping, I am getting only one histogram.


You're probably just plotting the file wrong.

xmgrace -nxy histo.xvg


Here I am sending the link that containing PMF profile and histogram that
have obtained.
http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg
http://researchweb.iiit.ac.in/~bipin.singh/hist.jpg



The PMF suggests massive undersampling (or complete lack of sampling) in several 
areas.



the weired thing that I have observed in my pulling simulations is that I
have expected motion of ion in positive Y-direction for my pull parameters
but it is moving in negative Y- direction.
  Can anybody please suggest me a solution for this,  Am I following correct
protocol to get PMF of my system, is there any better method that suits for
my system.



If you are trying to see a complete translocation of an ion through a channel, 
the "distance" geometry is inappropriate, as it does not deal correctly with the 
change of sign for the vector between the reference and pulled group, IIRC.  Try 
"position" geometry and associated settings.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
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