Re: [gmx-users] How to write pull code in umbrella sampling

2017-04-08 Thread Qing Lv 
Thank you so much, Justin. I will look into PLUMED.


Qing


At 2017-04-08 19:05:28, "Justin Lemkul"  wrote:
>
>
>On 4/8/17 1:46 AM, Qing Lv wrote:
>> Thank you, Justin.
>>
>>
>> My goal is to investigate the conformation transition of a 30aa loop between 
>> an unstructured loop and an alpha-helix. I found a transition pathway on 
>> free energy landscape and selected a number of frames along the pathway for 
>> umbrella sampling. So, should I define C-alpha of this 30aa loop as 
>> pull-group1 and C-alpha of the remaining part as pull-group2 ? Would the 
>> pull geometry still be "distance"? But this will just restrain the distance 
>> between COM of the 2 groups to the initial distance, but cannot restrain the 
>> conformation of the loop.
>> Or need I divide the loop into many small segments (pull-groups) and define 
>> the pull coordinates separately? This seems horrible...
>>
>
>You should probably be looking at a more advanced, multi-dimensional bias or 
>collective variable.  Look into PLUMED.  GROMACS is going to be limited to a 
>linear reaction coordinate, which may not capture everything you need in such 
>a 
>large transition.
>
>-Justin
>
>>
>> Thanks,
>> Qing
>>
>>
>> At 2017-04-08 09:06:46, "Justin Lemkul"  wrote:
>>>
>>>
>>> On 4/7/17 8:56 PM, Qing Lv wrote:
 Dear Colleagues,


 I am trying to do an umbrella sampling using a series of conformations 
 extracted from several unbiased MD trajectories. But I am not sure about 
 the pull code in .mdp file.
 Below is the pull code from the tutorial of Dr. Justin Lemkul :
 define  = -DPOSRES_B ; (Why ??)
>>>
>>> Did you read the paper I linked from the tutorial, which explains why this 
>>> is
>>> done for this very specific case?
>>>
 ; Pull code
 pull= yes
 pull_ngroups= 2
 pull_ncoords= 1
 pull_group1_name= Chain_B
 pull_group2_name= Chain_A
 pull_coord1_type= umbrella  ; harmonic biasing force
 pull_coord1_geometry= distance  ; simple distance increase
 pull_coord1_groups  = 1 2
 pull_coord1_dim = N N Y
 pull_coord1_rate= 0.0
 pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
 pull_coord1_start   = yes   ; define initial COM distance > 0



 Conformations in Justin's tutorial are from steered MD. However, my 
 conformations are not from SMD, and I have not done SMD on this system. 
 So, how to define pull_group1 and pull_group2? And pull_coord1_geometry 
 still set to "distance" ?
>>>
>>> The pull groups don't depend on where the configurations came from.  They 
>>> define
>>> the reaction coordinate.  You can use whatever pull geometry makes sense; 
>>> in the
>>> tutorial it is a simple linear reaction coordinate directly along the 
>>> z-axis.
>>> Other applications may require different definitions.
>>>
 Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES 
 ") ? Why?
>>>
>>> Generally, no, but you haven't given any useful detail about what your
>>> simulation system is.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send 
>>> a mail to gmx-users-requ...@gromacs.org.
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at

Re: [gmx-users] How to write pull code in umbrella sampling

2017-04-08 Thread Justin Lemkul 



On 4/8/17 1:46 AM, Qing Lv wrote:

Thank you, Justin.


My goal is to investigate the conformation transition of a 30aa loop between an 
unstructured loop and an alpha-helix. I found a transition pathway on free energy 
landscape and selected a number of frames along the pathway for umbrella sampling. So, 
should I define C-alpha of this 30aa loop as pull-group1 and C-alpha of the remaining 
part as pull-group2 ? Would the pull geometry still be "distance"? But this 
will just restrain the distance between COM of the 2 groups to the initial distance, but 
cannot restrain the conformation of the loop.
Or need I divide the loop into many small segments (pull-groups) and define the 
pull coordinates separately? This seems horrible...



You should probably be looking at a more advanced, multi-dimensional bias or 
collective variable.  Look into PLUMED.  GROMACS is going to be limited to a 
linear reaction coordinate, which may not capture everything you need in such a 
large transition.


-Justin



Thanks,
Qing


At 2017-04-08 09:06:46, "Justin Lemkul"  wrote:



On 4/7/17 8:56 PM, Qing Lv wrote:

Dear Colleagues,


I am trying to do an umbrella sampling using a series of conformations 
extracted from several unbiased MD trajectories. But I am not sure about the 
pull code in .mdp file.
Below is the pull code from the tutorial of Dr. Justin Lemkul :
define  = -DPOSRES_B ; (Why ??)


Did you read the paper I linked from the tutorial, which explains why this is
done for this very specific case?


; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0



Conformations in Justin's tutorial are from steered MD. However, my conformations are not 
from SMD, and I have not done SMD on this system. So, how to define pull_group1 and 
pull_group2? And pull_coord1_geometry still set to "distance" ?


The pull groups don't depend on where the configurations came from.  They define
the reaction coordinate.  You can use whatever pull geometry makes sense; in the
tutorial it is a simple linear reaction coordinate directly along the z-axis.
Other applications may require different definitions.


Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? 
Why?


Generally, no, but you haven't given any useful detail about what your
simulation system is.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How to write pull code in umbrella sampling

2017-04-07 Thread Qing Lv 
Thank you, Justin.


My goal is to investigate the conformation transition of a 30aa loop between an 
unstructured loop and an alpha-helix. I found a transition pathway on free 
energy landscape and selected a number of frames along the pathway for umbrella 
sampling. So, should I define C-alpha of this 30aa loop as pull-group1 and 
C-alpha of the remaining part as pull-group2 ? Would the pull geometry still be 
"distance"? But this will just restrain the distance between COM of the 2 
groups to the initial distance, but cannot restrain the conformation of the 
loop.
Or need I divide the loop into many small segments (pull-groups) and define the 
pull coordinates separately? This seems horrible...


Thanks,
Qing


At 2017-04-08 09:06:46, "Justin Lemkul"  wrote:
>
>
>On 4/7/17 8:56 PM, Qing Lv wrote:
>> Dear Colleagues,
>>
>>
>> I am trying to do an umbrella sampling using a series of conformations 
>> extracted from several unbiased MD trajectories. But I am not sure about the 
>> pull code in .mdp file.
>> Below is the pull code from the tutorial of Dr. Justin Lemkul :
>> define  = -DPOSRES_B ; (Why ??)
>
>Did you read the paper I linked from the tutorial, which explains why this is 
>done for this very specific case?
>
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= Chain_B
>> pull_group2_name= Chain_A
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>>
>>
>> Conformations in Justin's tutorial are from steered MD. However, my 
>> conformations are not from SMD, and I have not done SMD on this system. So, 
>> how to define pull_group1 and pull_group2? And pull_coord1_geometry still 
>> set to "distance" ?
>
>The pull groups don't depend on where the configurations came from.  They 
>define 
>the reaction coordinate.  You can use whatever pull geometry makes sense; in 
>the 
>tutorial it is a simple linear reaction coordinate directly along the z-axis. 
>Other applications may require different definitions.
>
>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES 
>> ") ? Why?
>
>Generally, no, but you haven't given any useful detail about what your 
>simulation system is.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] How to write pull code in umbrella sampling

2017-04-07 Thread Qing Lv 
Dear Colleagues,


I am trying to do an umbrella sampling using a series of conformations 
extracted from several unbiased MD trajectories. But I am not sure about the 
pull code in .mdp file.
Below is the pull code from the tutorial of Dr. Justin Lemkul :
define  = -DPOSRES_B ; (Why ??)
; Pull code 
pull= yes   
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.0
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0



Conformations in Justin's tutorial are from steered MD. However, my 
conformations are not from SMD, and I have not done SMD on this system. So, how 
to define pull_group1 and pull_group2? And pull_coord1_geometry still set to 
"distance" ?
Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? 
Why?
Any one can provide a template of pull code for such simulations?


Thanks a lot
Qing Lv


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.