Re: [gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Does anyone have proper parameters for CNTs ? I have been trying to perform
Simulations with finite CNTs. However, none of the parameters so far
(obtained from literature) seem to give the output temperatures equal to
set temperatures.

I have been looked into my input files time and again, but I could not
locate any bug so far. The problem is if I simulate my CNT with bonds
angles dihedrals and 1-4 interactions and constraint the bonds, the
temperature of the CNT seems to deviate far from the set temperature with
reasonable values of tau-t using the sd integrator in GROMACS.

Does anyone have parameters for CNTs such that they work with the SD
integrator with reasonable tau-t values?


On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER  wrote:

> @Vitaly. Yes you are right. However, I noticed that if I do not constraint
> the bonds in my CNT my simulations run fine. It is indeed surprising to me
> but I do not have much experience with simulating CNTs and if not
> constraining the bonds seem to get things done, I think it is a viable
> option. But still need to test a lot of things before I can decide on the
> final settings.
>
>
> On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER <
> hanniballecte...@gmail.com> wrote:
>
>> Yes. That is the way to go about it. I was hoping for a more lazy
>> approach... Thanks anyways.
>>
>>
>> On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>>>
 Is there a smart way of writing the constraint sections in the topology
 file other than entering the values manually ?


>>> Write a script that parses the [bonds] directive of the post-processed
>>> topology (output by grompp -pp) and write the relevant fields to a
>>> [constraints] directive.
>>>
>>> -Justin
>>>
>>>
>>>
 On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
 **wrote:

  Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul 
> wrote:
>
>
>>
>> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>>
>>  Is there a way to constraint bonds of a part of the system while
>>> keeping
>>> the other part flexible? For example for a simulation with two
>>>
>> proteins, I
>
>> would like to constraint the bonds of one and would like to keep the
>>>
>> other
>
>> flexible.
>>>
>>> I would prefer to use LINCS to constraint the system
>>>
>>>
>>>  Set the constraints explicitly in the topology of one protein using
>> a
>> [constraints] directive.  Then set "constraints = none" in the .mdp
>> file.
>>   The constraints read from the topology will override the .mdp
>> setting
>> while leaving all other bonds unconstrained.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.edu > umaryland.edu >
>>
> | (410)
>
>> 706-7441
>>
>> ==
>>
>> --
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Re: [gmx-users] Constraining a part of the system

[Dr. Vitaly Chaban]

the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban


On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
 wrote:
> Is there a smart way of writing the constraint sections in the topology
> file other than entering the values manually ?
>
>
> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
> wrote:
>
>> Thanks
>>
>>
>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>> >
>> >> Is there a way to constraint bonds of a part of the system while keeping
>> >> the other part flexible? For example for a simulation with two
>> proteins, I
>> >> would like to constraint the bonds of one and would like to keep the
>> other
>> >> flexible.
>> >>
>> >> I would prefer to use LINCS to constraint the system
>> >>
>> >>
>> > Set the constraints explicitly in the topology of one protein using a
>> > [constraints] directive.  Then set "constraints = none" in the .mdp file.
>> >  The constraints read from the topology will override the .mdp setting
>> > while leaving all other bonds unconstrained.
>> >
>> > -Justin
>> >
>> > --
>> > ==**
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Postdoctoral Fellow
>> >
>> > Department of Pharmaceutical Sciences
>> > School of Pharmacy
>> > Health Sciences Facility II, Room 601
>> > University of Maryland, Baltimore
>> > 20 Penn St.
>> > Baltimore, MD 21201
>> >
>> > jalemkul@outerbanks.umaryland.**edu 
>> | (410)
>> > 706-7441
>> >
>> > ==**
>> >
>> > --
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Re: [gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?


On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
wrote:

> Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
> >
> >> Is there a way to constraint bonds of a part of the system while keeping
> >> the other part flexible? For example for a simulation with two
> proteins, I
> >> would like to constraint the bonds of one and would like to keep the
> other
> >> flexible.
> >>
> >> I would prefer to use LINCS to constraint the system
> >>
> >>
> > Set the constraints explicitly in the topology of one protein using a
> > [constraints] directive.  Then set "constraints = none" in the .mdp file.
> >  The constraints read from the topology will override the .mdp setting
> > while leaving all other bonds unconstrained.
> >
> > -Justin
> >
> > --
> > ==**
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul@outerbanks.umaryland.**edu 
> | (410)
> > 706-7441
> >
> > ==**
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
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Re: [gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.


On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:

>
>
> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>
>> Is there a smart way of writing the constraint sections in the topology
>> file other than entering the values manually ?
>>
>>
> Write a script that parses the [bonds] directive of the post-processed
> topology (output by grompp -pp) and write the relevant fields to a
> [constraints] directive.
>
> -Justin
>
>
>
>> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
>> **wrote:
>>
>>  Thanks
>>>
>>>
>>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>>>
>>>

 On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:

  Is there a way to constraint bonds of a part of the system while
> keeping
> the other part flexible? For example for a simulation with two
>
 proteins, I
>>>
 would like to constraint the bonds of one and would like to keep the
>
 other
>>>
 flexible.
>
> I would prefer to use LINCS to constraint the system
>
>
>  Set the constraints explicitly in the topology of one protein using a
 [constraints] directive.  Then set "constraints = none" in the .mdp
 file.
   The constraints read from the topology will override the .mdp setting
 while leaving all other bonds unconstrained.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalemkul@outerbanks.umaryland.edu >>> umaryland.edu >

>>> | (410)
>>>
 706-7441

 ==

 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
 <

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 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Search<

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>>>
> --
> ==**
>
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
>
> --
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Re: [gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

@Vitaly. Yes you are right. However, I noticed that if I do not constraint
the bonds in my CNT my simulations run fine. It is indeed surprising to me
but I do not have much experience with simulating CNTs and if not
constraining the bonds seem to get things done, I think it is a viable
option. But still need to test a lot of things before I can decide on the
final settings.


On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER  wrote:

> Yes. That is the way to go about it. I was hoping for a more lazy
> approach... Thanks anyways.
>
>
> On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>>
>>> Is there a smart way of writing the constraint sections in the topology
>>> file other than entering the values manually ?
>>>
>>>
>> Write a script that parses the [bonds] directive of the post-processed
>> topology (output by grompp -pp) and write the relevant fields to a
>> [constraints] directive.
>>
>> -Justin
>>
>>
>>
>>> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
>>> **wrote:
>>>
>>>  Thanks


 On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul 
 wrote:


>
> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>
>  Is there a way to constraint bonds of a part of the system while
>> keeping
>> the other part flexible? For example for a simulation with two
>>
> proteins, I

> would like to constraint the bonds of one and would like to keep the
>>
> other

> flexible.
>>
>> I would prefer to use LINCS to constraint the system
>>
>>
>>  Set the constraints explicitly in the topology of one protein using a
> [constraints] directive.  Then set "constraints = none" in the .mdp
> file.
>   The constraints read from the topology will override the .mdp setting
> while leaving all other bonds unconstrained.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.edu  umaryland.edu >
>
 | (410)

> 706-7441
>
> ==
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> <
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 http://lists.gromacs.org/**mailman/listinfo/gmx-users
 >

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>> --
>> ==**
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu | 
>> (410)
>> 706-7441
>>
>> ==**
>>
>> --
>> 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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>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists

Re: [gmx-users] Constraining a part of the system

[Justin Lemkul]

On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:

Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?



Write a script that parses the [bonds] directive of the post-processed topology 
(output by grompp -pp) and write the relevant fields to a [constraints] directive.


-Justin



On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
wrote:


Thanks


On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:




On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:


Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two

proteins, I

would like to constraint the bonds of one and would like to keep the

other

flexible.

I would prefer to use LINCS to constraint the system



Set the constraints explicitly in the topology of one protein using a
[constraints] directive.  Then set "constraints = none" in the .mdp file.
  The constraints read from the topology will override the .mdp setting
while leaving all other bonds unconstrained.

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu 

| (410)

706-7441

==**

--
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Constraining a part of the system

[Justin Lemkul]

On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:

Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.

I would prefer to use LINCS to constraint the system



Set the constraints explicitly in the topology of one protein using a 
[constraints] directive.  Then set "constraints = none" in the .mdp file.  The 
constraints read from the topology will override the .mdp setting while leaving 
all other bonds unconstrained.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.

I would prefer to use LINCS to constraint the system
-- 
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Re: [gmx-users] Constraining a part of the system

[rahul seth]

Thanks


On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:

>
>
> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>
>> Is there a way to constraint bonds of a part of the system while keeping
>> the other part flexible? For example for a simulation with two proteins, I
>> would like to constraint the bonds of one and would like to keep the other
>> flexible.
>>
>> I would prefer to use LINCS to constraint the system
>>
>>
> Set the constraints explicitly in the topology of one protein using a
> [constraints] directive.  Then set "constraints = none" in the .mdp file.
>  The constraints read from the topology will override the .mdp setting
> while leaving all other bonds unconstrained.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
>
> --
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