Re: [gmx-users] PMF calculation_ Constraint

2015-09-23 Thread Sepideh Kavousi 
Dear Justin.
Thanks for response. I used constraint method because I wanted to calculate
MSD, How does using a bigger box helps me? because when  I make box bigger,
I need to run a little bit to equilibrate system, and again the tocopherol
can move and come out of the box.

On Tue, Sep 22, 2015 at 5:45 PM, Justin Lemkul  wrote:

>
>
> On 9/22/15 3:46 PM, Sepideh Kavousi wrote:
>
>> Dear Gromacs users
>>
>> I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
>> means, I used Constraint method. the pull code in my .mdp file is :
>>
>> pull = constraint
>> pull-geometry = distance;distance, direction, or cylinder
>> pull-dim = N N Y
>> pull-constr-tol = 1e-6
>> pull-start = yes;add current COM distance to
>> pull_init?
>> pull-print-reference = no
>> pull-nstxout = 1
>> pull-nstfout = 5
>> pull-ngroups = 2
>> pull-ncoords = 1
>> pull-group1-name = DMPC
>> pull-group2-name = VIT
>> pull-coord1-groups = 1 2
>> pull-coord1-init = 0.0
>>
>>
>> In my output file which shows force over time, we have some sudden
>> diverges
>> of force to a very high number.
>> I realized it is because of the boundary condition, one part of molecule
>> comes out of the box and enters from the other side of the box and it
>> needs
>> a huge force to keep the molecule at the same position. Can you please
>> help
>> me how to solve this problem
>>
>>
> Use a bigger box, use a shorter reaction coordinate, or use an umbrella
> sampling method that supports PBC.  I suspect any output using the
> constraint method will be very poorly converged.
>
> -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
>
> ==
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> Gromacs Users mailing list
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[gmx-users] PMF calculation_ Constraint

2015-09-22 Thread Sepideh Kavousi 
Dear Gromacs users

I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
means, I used Constraint method. the pull code in my .mdp file is :

pull = constraint
pull-geometry = distance;distance, direction, or cylinder
pull-dim = N N Y
pull-constr-tol = 1e-6
pull-start = yes;add current COM distance to pull_init?
pull-print-reference = no
pull-nstxout = 1
pull-nstfout = 5
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = DMPC
pull-group2-name = VIT
pull-coord1-groups = 1 2
pull-coord1-init = 0.0


In my output file which shows force over time, we have some sudden diverges
of force to a very high number.
I realized it is because of the boundary condition, one part of molecule
comes out of the box and enters from the other side of the box and it needs
a huge force to keep the molecule at the same position. Can you please help
me how to solve this problem
-- 
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Re: [gmx-users] PMF calculation_ Constraint

2015-09-22 Thread Justin Lemkul 



On 9/22/15 3:46 PM, Sepideh Kavousi wrote:

Dear Gromacs users

I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
means, I used Constraint method. the pull code in my .mdp file is :

pull = constraint
pull-geometry = distance;distance, direction, or cylinder
pull-dim = N N Y
pull-constr-tol = 1e-6
pull-start = yes;add current COM distance to pull_init?
pull-print-reference = no
pull-nstxout = 1
pull-nstfout = 5
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = DMPC
pull-group2-name = VIT
pull-coord1-groups = 1 2
pull-coord1-init = 0.0


In my output file which shows force over time, we have some sudden diverges
of force to a very high number.
I realized it is because of the boundary condition, one part of molecule
comes out of the box and enters from the other side of the box and it needs
a huge force to keep the molecule at the same position. Can you please help
me how to solve this problem



Use a bigger box, use a shorter reaction coordinate, or use an umbrella sampling 
method that supports PBC.  I suspect any output using the constraint method will 
be very poorly converged.


-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

==
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