Re: [gmx-users] PMF and lack if NPT equilibration

[Alex]

Thanks.

I used the "direction-periodic",  along with "semiisotropic" with zero
compressibility in Z direction to have also NPT equilibration in each
windows. Below is the final pressure after NPT equilibration with 1 bar
reference, I hope it would be ok?!

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -252.127   0.66165.0533.15753  (bar)

Regards,
Alex


On Mon, Oct 10, 2016 at 8:25 PM, Justin Lemkul  wrote:

>
>
> On 10/10/16 4:57 AM, Alex wrote:
>
>> Thanks for your response.
>>
>> My question is not in the sampling step as I have already pulled away two
>> parts and even picked out the configuration of each windows. But my
>> question is about simulation in each individual windows toward WHAM.
>>
>> You means in the step six of the tutorial no necessarily need to do any
>> NVT
>> or NPT before production simulation?
>>
>>
> It's no different from any simulation.  You need to equilibrate under the
> ensemble you're going to use for data collection before you actually do
> that data collection.  If you would normally want NPT for a Gibbs free
> energy and can't get it for whatever reason (like the algorithmic
> limitation mentioned), then equilibrate with NPT to arrive at the desired
> density, and continue with NVT.  You won't get a Gibbs free energy, you'll
> get the Helmholtz free energy, but at least the density will be right.
> Otherwise, build a bigger system that removes the restrictions of
> direction_periodic and use NPT.
>
> -Justin
>
>
> Thanks,
>> Alex
>>
>>
>> On Mon, Oct 10, 2016 at 2:17 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/8/16 2:46 PM, Alex wrote:
>>>
>>> Dear gromacs user,

 In a PMF simulation of a short peptide on solid surface, I am using the
 "direction-periodic" as "pull-coord1-geometry" in the Z  direction, then
 as
 you know the equilibration of the system in NPT ensemble is not doable
 for
 the individual windows. So, for each windows of umbrella sampling, I am
 going to do minimization and NVT equilibration and then MD production. I
 was wondering if the lack of the NPT  equilibration would not badly
 affect
 on the result PMF? If so, how can I compensate it somehow?


 All you're doing is sampling under a different ensemble.  There's no
>>> reason to think that a PMF requires an NPT ensemble.
>>>
>>> -Justin
>>>
>>> By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60
>>> ns
>>>
 of production simulation of my initial system before coming to the
 pulling
 step.

 Thanks.

 Regards,
 Alex


 --
>>> ==
>>>
>>> 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 
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] PMF and lack if NPT equilibration

[Justin Lemkul]

On 10/10/16 4:57 AM, Alex wrote:

Thanks for your response.

My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.

You means in the step six of the tutorial no necessarily need to do any NVT
or NPT before production simulation?



It's no different from any simulation.  You need to equilibrate under the 
ensemble you're going to use for data collection before you actually do that 
data collection.  If you would normally want NPT for a Gibbs free energy and 
can't get it for whatever reason (like the algorithmic limitation mentioned), 
then equilibrate with NPT to arrive at the desired density, and continue with 
NVT.  You won't get a Gibbs free energy, you'll get the Helmholtz free energy, 
but at least the density will be right.  Otherwise, build a bigger system that 
removes the restrictions of direction_periodic and use NPT.


-Justin


Thanks,
Alex


On Mon, Oct 10, 2016 at 2:17 AM, Justin Lemkul  wrote:




On 10/8/16 2:46 PM, Alex wrote:


Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then
as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly affect
on the result PMF? If so, how can I compensate it somehow?



All you're doing is sampling under a different ensemble.  There's no
reason to think that a PMF requires an NPT ensemble.

-Justin

By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns

of production simulation of my initial system before coming to the pulling
step.

Thanks.

Regards,
Alex



--
==

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] PMF and lack if NPT equilibration

[Alex]

Thanks for your response.

My question is not in the sampling step as I have already pulled away two
parts and even picked out the configuration of each windows. But my
question is about simulation in each individual windows toward WHAM.

You means in the step six of the tutorial no necessarily need to do any NVT
or NPT before production simulation?

Thanks,
Alex


On Mon, Oct 10, 2016 at 2:17 AM, Justin Lemkul  wrote:

>
>
> On 10/8/16 2:46 PM, Alex wrote:
>
>> Dear gromacs user,
>>
>> In a PMF simulation of a short peptide on solid surface, I am using the
>> "direction-periodic" as "pull-coord1-geometry" in the Z  direction, then
>> as
>> you know the equilibration of the system in NPT ensemble is not doable for
>> the individual windows. So, for each windows of umbrella sampling, I am
>> going to do minimization and NVT equilibration and then MD production. I
>> was wondering if the lack of the NPT  equilibration would not badly affect
>> on the result PMF? If so, how can I compensate it somehow?
>>
>>
> All you're doing is sampling under a different ensemble.  There's no
> reason to think that a PMF requires an NPT ensemble.
>
> -Justin
>
> By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
>> of production simulation of my initial system before coming to the pulling
>> step.
>>
>> Thanks.
>>
>> Regards,
>> Alex
>>
>>
> --
> ==
>
> 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.

Re: [gmx-users] PMF and lack if NPT equilibration

[Justin Lemkul]

On 10/8/16 2:46 PM, Alex wrote:

Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly affect
on the result PMF? If so, how can I compensate it somehow?



All you're doing is sampling under a different ensemble.  There's no reason to 
think that a PMF requires an NPT ensemble.


-Justin


By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
of production simulation of my initial system before coming to the pulling
step.

Thanks.

Regards,
Alex



--
==

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.

[gmx-users] PMF and lack if NPT equilibration

[Alex]

Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly affect
on the result PMF? If so, how can I compensate it somehow?

By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
of production simulation of my initial system before coming to the pulling
step.

Thanks.

Regards,
Alex
-- 
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.