Re: [gmx-users] Gromacs 2016 pull options

2017-02-20 Thread Justin Lemkul 



On 2/20/17 8:24 AM, Gmx QA wrote:

Ah, ok, so the rate does not specify the velocity by which the pull-group
moves?



No.  Motion of the groups depends on the forces, not the velocity at which the 
virtual spring moves.



Does it have the same function in the case of constant-force pulling?



No, and there are important differences in the way options are specified for 
constant velocity and constant force pulling.  See the link I provided, where 
all of that is described.


-Justin


2017-02-20 14:20 GMT+01:00 Justin Lemkul :




On 2/20/17 8:19 AM, Gmx QA wrote:


Hi Justin

Thank you for your response.

I will test that obviously, but just for my understanding then:
Is it not enough to specify the pull-coord1-rate, you also need the
pull-coord1-k to make it work?

They seem to be specifying sort of the same thing really…



The rate is the velocity at which the biasing spring extends.  The force
constant calculates how much force is thus applied to the restrained groups
based on that displacement.  They are independent of one another,
functionally and mathematically.

-Justin


Thanks

/PK

2017-02-20 14:13 GMT+01:00 Justin Lemkul :




On 2/20/17 8:09 AM, Gmx QA wrote:

Dear list


Could someone please clarify a few issues I have with the 2016 version
of
the pull code. Or rather, explain why the below approach is not working.

I am trying to pull a small molecule though a bilayer. Initially, the
drug
is "below" the membrane, i e has a smaller z-coordinate, so I want to
pull
in the positive z direction through the membrane.

The following is a snippet of my mdp-file, with the relevant parts for
the
pull specs.

pull  = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups   = 1 2
pull-group1-name = drug
pull-group2-name = membrane
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec  = 0 0 1
pull-coord1-rate = 0.1

This I think should define two pull groups,one for the drug and one for
the
membrane, and it should pull the drug molecule with pull-coord1-rate in
positive z. I am using direction-periodic since I expect to pull more
than
half the box z length.

When I test this, running a 1 ns simulation, during which I expect the
drug
to be pulled a significant way, nothing really happens with the com of
the
drug, it just "sits" out in the water phase.


You didn't set a value of pull-coord1-k, so it defaults to zero and

therefore you get no biasing potential.

http://manual.gromacs.org/documentation/2016.2/user-guide/
mdp-options.html#com-pulling

-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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--
==

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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--
==

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] Gromacs 2016 pull options

2017-02-20 Thread Gmx QA 
Ah, ok, so the rate does not specify the velocity by which the pull-group
moves?

Does it have the same function in the case of constant-force pulling?

2017-02-20 14:20 GMT+01:00 Justin Lemkul :

>
>
> On 2/20/17 8:19 AM, Gmx QA wrote:
>
>> Hi Justin
>>
>> Thank you for your response.
>>
>> I will test that obviously, but just for my understanding then:
>> Is it not enough to specify the pull-coord1-rate, you also need the
>> pull-coord1-k to make it work?
>>
>> They seem to be specifying sort of the same thing really…
>>
>>
> The rate is the velocity at which the biasing spring extends.  The force
> constant calculates how much force is thus applied to the restrained groups
> based on that displacement.  They are independent of one another,
> functionally and mathematically.
>
> -Justin
>
>
> Thanks
>> /PK
>>
>> 2017-02-20 14:13 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 2/20/17 8:09 AM, Gmx QA wrote:
>>>
>>> Dear list

 Could someone please clarify a few issues I have with the 2016 version
 of
 the pull code. Or rather, explain why the below approach is not working.

 I am trying to pull a small molecule though a bilayer. Initially, the
 drug
 is "below" the membrane, i e has a smaller z-coordinate, so I want to
 pull
 in the positive z direction through the membrane.

 The following is a snippet of my mdp-file, with the relevant parts for
 the
 pull specs.

 pull  = yes
 pull-ngroups = 2
 pull-ncoords = 1
 pull-coord1-groups   = 1 2
 pull-group1-name = drug
 pull-group2-name = membrane
 pull-coord1-type = umbrella
 pull-coord1-geometry = direction-periodic
 pull-coord1-vec  = 0 0 1
 pull-coord1-rate = 0.1

 This I think should define two pull groups,one for the drug and one for
 the
 membrane, and it should pull the drug molecule with pull-coord1-rate in
 positive z. I am using direction-periodic since I expect to pull more
 than
 half the box z length.

 When I test this, running a 1 ns simulation, during which I expect the
 drug
 to be pulled a significant way, nothing really happens with the com of
 the
 drug, it just "sits" out in the water phase.


 You didn't set a value of pull-coord1-k, so it defaults to zero and
>>> therefore you get no biasing potential.
>>>
>>> http://manual.gromacs.org/documentation/2016.2/user-guide/
>>> mdp-options.html#com-pulling
>>>
>>> -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.
>
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Re: [gmx-users] Gromacs 2016 pull options

2017-02-20 Thread Justin Lemkul 



On 2/20/17 8:19 AM, Gmx QA wrote:

Hi Justin

Thank you for your response.

I will test that obviously, but just for my understanding then:
Is it not enough to specify the pull-coord1-rate, you also need the
pull-coord1-k to make it work?

They seem to be specifying sort of the same thing really…



The rate is the velocity at which the biasing spring extends.  The force 
constant calculates how much force is thus applied to the restrained groups 
based on that displacement.  They are independent of one another, functionally 
and mathematically.


-Justin


Thanks
/PK

2017-02-20 14:13 GMT+01:00 Justin Lemkul :




On 2/20/17 8:09 AM, Gmx QA wrote:


Dear list

Could someone please clarify a few issues I have with the 2016 version of
the pull code. Or rather, explain why the below approach is not working.

I am trying to pull a small molecule though a bilayer. Initially, the drug
is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
in the positive z direction through the membrane.

The following is a snippet of my mdp-file, with the relevant parts for the
pull specs.

pull  = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups   = 1 2
pull-group1-name = drug
pull-group2-name = membrane
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec  = 0 0 1
pull-coord1-rate = 0.1

This I think should define two pull groups,one for the drug and one for
the
membrane, and it should pull the drug molecule with pull-coord1-rate in
positive z. I am using direction-periodic since I expect to pull more than
half the box z length.

When I test this, running a 1 ns simulation, during which I expect the
drug
to be pulled a significant way, nothing really happens with the com of the
drug, it just "sits" out in the water phase.



You didn't set a value of pull-coord1-k, so it defaults to zero and
therefore you get no biasing potential.

http://manual.gromacs.org/documentation/2016.2/user-guide/
mdp-options.html#com-pulling

-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

* Please search the archive at http://www.gromacs.org/Support
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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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Gromacs 2016 pull options

2017-02-20 Thread Gmx QA 
Hi Justin

Thank you for your response.

I will test that obviously, but just for my understanding then:
Is it not enough to specify the pull-coord1-rate, you also need the
pull-coord1-k to make it work?

They seem to be specifying sort of the same thing really…

Thanks
/PK

2017-02-20 14:13 GMT+01:00 Justin Lemkul :

>
>
> On 2/20/17 8:09 AM, Gmx QA wrote:
>
>> Dear list
>>
>> Could someone please clarify a few issues I have with the 2016 version of
>> the pull code. Or rather, explain why the below approach is not working.
>>
>> I am trying to pull a small molecule though a bilayer. Initially, the drug
>> is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
>> in the positive z direction through the membrane.
>>
>> The following is a snippet of my mdp-file, with the relevant parts for the
>> pull specs.
>>
>> pull  = yes
>> pull-ngroups = 2
>> pull-ncoords = 1
>> pull-coord1-groups   = 1 2
>> pull-group1-name = drug
>> pull-group2-name = membrane
>> pull-coord1-type = umbrella
>> pull-coord1-geometry = direction-periodic
>> pull-coord1-vec  = 0 0 1
>> pull-coord1-rate = 0.1
>>
>> This I think should define two pull groups,one for the drug and one for
>> the
>> membrane, and it should pull the drug molecule with pull-coord1-rate in
>> positive z. I am using direction-periodic since I expect to pull more than
>> half the box z length.
>>
>> When I test this, running a 1 ns simulation, during which I expect the
>> drug
>> to be pulled a significant way, nothing really happens with the com of the
>> drug, it just "sits" out in the water phase.
>>
>>
> You didn't set a value of pull-coord1-k, so it defaults to zero and
> therefore you get no biasing potential.
>
> http://manual.gromacs.org/documentation/2016.2/user-guide/
> mdp-options.html#com-pulling
>
> -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.
>
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Re: [gmx-users] Gromacs 2016 pull options

2017-02-20 Thread Justin Lemkul 



On 2/20/17 8:09 AM, Gmx QA wrote:

Dear list

Could someone please clarify a few issues I have with the 2016 version of
the pull code. Or rather, explain why the below approach is not working.

I am trying to pull a small molecule though a bilayer. Initially, the drug
is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
in the positive z direction through the membrane.

The following is a snippet of my mdp-file, with the relevant parts for the
pull specs.

pull  = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups   = 1 2
pull-group1-name = drug
pull-group2-name = membrane
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec  = 0 0 1
pull-coord1-rate = 0.1

This I think should define two pull groups,one for the drug and one for the
membrane, and it should pull the drug molecule with pull-coord1-rate in
positive z. I am using direction-periodic since I expect to pull more than
half the box z length.

When I test this, running a 1 ns simulation, during which I expect the drug
to be pulled a significant way, nothing really happens with the com of the
drug, it just "sits" out in the water phase.



You didn't set a value of pull-coord1-k, so it defaults to zero and therefore 
you get no biasing potential.


http://manual.gromacs.org/documentation/2016.2/user-guide/mdp-options.html#com-pulling

-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] Gromacs 2016 pull options

2017-02-20 Thread Gmx QA 
Dear list

Could someone please clarify a few issues I have with the 2016 version of
the pull code. Or rather, explain why the below approach is not working.

I am trying to pull a small molecule though a bilayer. Initially, the drug
is "below" the membrane, i e has a smaller z-coordinate, so I want to pull
in the positive z direction through the membrane.

The following is a snippet of my mdp-file, with the relevant parts for the
pull specs.

pull  = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups   = 1 2
pull-group1-name = drug
pull-group2-name = membrane
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec  = 0 0 1
pull-coord1-rate = 0.1

This I think should define two pull groups,one for the drug and one for the
membrane, and it should pull the drug molecule with pull-coord1-rate in
positive z. I am using direction-periodic since I expect to pull more than
half the box z length.

When I test this, running a 1 ns simulation, during which I expect the drug
to be pulled a significant way, nothing really happens with the com of the
drug, it just "sits" out in the water phase.

Please advice!
/PK
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