Re: [gmx-users] Velocity Verlet integrator
Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Maybe I am missunderstanding something. Thank you very much, Mario Fernández-Pendás 2014-03-23 14:33 GMT+01:00 Michael Shirts mrshi...@gmail.com: Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns out to be non-trivial for the bookkeeping. The easiest way to do this was split the velocity Verlet updates. Also, the additional computational cost of two half steps for velocities is trivial compared to the cost of the forces for almost all systems. On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás mariof...@gmail.com wrote: Dear all, In terms of computational efficiency, why the velocity Verlet integrator is implemented in GROMACS in one full step for positions and two half steps for velocities? Would it be more efficient to merge the second halft step for velocities with the first half step of the following scheme, ie, integrating in one full step for velocities? Thank you very much, Mario Fernánez-Pendás -- 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. -- 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] Velocity Verlet integrator
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote: Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Yes, there are two separate half-step updates for velocities. The comments in the md.cpp code are quite verbose if you want to trace through. -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.
Re: [gmx-users] Velocity Verlet integrator
Yes, I understand that. But my question is more about why the two velocity
updates are implemented before the position update and not the other way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) + \vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to
split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are two updates for velocities and then the update for
positions?
My intuitive idea would be to update first one half for velocities, then a
full step for positions and, finally, using these new positions the second
half for velocities.
Yes, there are two separate half-step updates for velocities. The
comments in the md.cpp code are quite verbose if you want to trace through.
-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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Re: [gmx-users] Velocity Verlet integrator
Because the 'start' of the vv integrator step is halfway through the loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the same
loop and 2) minimizing communication and output. It is not as elegant as
it should be. There are efforts to clean this up, but it's a lot of
reorganization, and has gone slowly.
On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás mariof...@gmail.com
wrote:
Yes, I understand that. But my question is more about why the two velocity
updates are implemented before the position update and not the other way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) + \vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to
split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are two updates for velocities and then the update for
positions?
My intuitive idea would be to update first one half for velocities,
then a
full step for positions and, finally, using these new positions the
second
half for velocities.
Yes, there are two separate half-step updates for velocities. The
comments in the md.cpp code are quite verbose if you want to trace
through.
-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!
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Re: [gmx-users] Velocity Verlet integrator
Thank you very much Professor Shirts.
I have these doubts because I am trying to implement new integrators based
in the concatenation of two VV steps to make a single step. The idea
follows the integrators suggested in
http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
This is why it is important for me to know where each step starts and
finishes.
2014-10-15 15:52 GMT+02:00 Michael Shirts mrshi...@gmail.com:
Because the 'start' of the vv integrator step is halfway through the loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the same
loop and 2) minimizing communication and output. It is not as elegant as
it should be. There are efforts to clean this up, but it's a lot of
reorganization, and has gone slowly.
On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás
mariof...@gmail.com
wrote:
Yes, I understand that. But my question is more about why the two
velocity
updates are implemented before the position update and not the other way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to
split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are two updates for velocities and then the update
for
positions?
My intuitive idea would be to update first one half for velocities,
then a
full step for positions and, finally, using these new positions the
second
half for velocities.
Yes, there are two separate half-step updates for velocities. The
comments in the md.cpp code are quite verbose if you want to trace
through.
-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!
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Re: [gmx-users] Velocity Verlet integrator
Yes, I've been using the theory here:
http://arxiv.org/abs/1301.3800
Which describes how to concantenate integrator steps in a formal way.
I can say that the time savings you get by concatenating integrators is
VERY small. The only time it is nonnegligible is when there is a LOT of
communication, and even then, there are better ways to make simulations
faster. It's not an area where there is a lot of improvement that can be
made.
When doing temperature and pressure control, there are many cases that you
cannot really join the steps as well.
On Wed, Oct 15, 2014 at 10:05 AM, Mario Fernández Pendás
mariof...@gmail.com wrote:
Thank you very much Professor Shirts.
I have these doubts because I am trying to implement new integrators based
in the concatenation of two VV steps to make a single step. The idea
follows the integrators suggested in
http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
This is why it is important for me to know where each step starts and
finishes.
2014-10-15 15:52 GMT+02:00 Michael Shirts mrshi...@gmail.com:
Because the 'start' of the vv integrator step is halfway through the
loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the
same
loop and 2) minimizing communication and output. It is not as elegant as
it should be. There are efforts to clean this up, but it's a lot of
reorganization, and has gone slowly.
On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás
mariof...@gmail.com
wrote:
Yes, I understand that. But my question is more about why the two
velocity
updates are implemented before the position update and not the other
way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta
t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was
to
split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are two updates for velocities and then the update
for
positions?
My intuitive idea would be to update first one half for velocities,
then a
full step for positions and, finally, using these new positions the
second
half for velocities.
Yes, there are two separate half-step updates for velocities. The
comments in the md.cpp code are quite verbose if you want to trace
through.
-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!
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Re: [gmx-users] Velocity Verlet integrator
Thank you very much for this reference. I will take a look at it carefully.
We are trying to develop and implement this integrators for hybrid Monte
Carlo simulations and our interest is not really related to time saving but
to sampling efficiency.
Right now it doesn't look straightforward to me to adapt GROMACS to this
integration schemes.
2014-10-15 17:05 GMT+02:00 Michael Shirts mrshi...@gmail.com:
Yes, I've been using the theory here:
http://arxiv.org/abs/1301.3800
Which describes how to concantenate integrator steps in a formal way.
I can say that the time savings you get by concatenating integrators is
VERY small. The only time it is nonnegligible is when there is a LOT of
communication, and even then, there are better ways to make simulations
faster. It's not an area where there is a lot of improvement that can be
made.
When doing temperature and pressure control, there are many cases that you
cannot really join the steps as well.
On Wed, Oct 15, 2014 at 10:05 AM, Mario Fernández Pendás
mariof...@gmail.com wrote:
Thank you very much Professor Shirts.
I have these doubts because I am trying to implement new integrators
based
in the concatenation of two VV steps to make a single step. The idea
follows the integrators suggested in
http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
This is why it is important for me to know where each step starts and
finishes.
2014-10-15 15:52 GMT+02:00 Michael Shirts mrshi...@gmail.com:
Because the 'start' of the vv integrator step is halfway through the
loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the
same
loop and 2) minimizing communication and output. It is not as elegant
as
it should be. There are efforts to clean this up, but it's a lot of
reorganization, and has gone slowly.
On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás
mariof...@gmail.com
wrote:
Yes, I understand that. But my question is more about why the two
velocity
updates are implemented before the position update and not the other
way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta
t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul jalem...@vt.edu:
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was
to
split
the updates in two updates. But I don't understad the order of
those
updates.
I mean why there are two updates for velocities and then the
update
for
positions?
My intuitive idea would be to update first one half for
velocities,
then a
full step for positions and, finally, using these new positions
the
second
half for velocities.
Yes, there are two separate half-step updates for velocities. The
comments in the md.cpp code are quite verbose if you want to trace
through.
-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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* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Velocity Verlet integrator
Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns out to be non-trivial for the bookkeeping. The easiest way to do this was split the velocity Verlet updates. Also, the additional computational cost of two half steps for velocities is trivial compared to the cost of the forces for almost all systems. On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás mariof...@gmail.com wrote: Dear all, In terms of computational efficiency, why the velocity Verlet integrator is implemented in GROMACS in one full step for positions and two half steps for velocities? Would it be more efficient to merge the second halft step for velocities with the first half step of the following scheme, ie, integrating in one full step for velocities? Thank you very much, Mario Fernánez-Pendás -- 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.
