Re: [gmx-users] Block averaging

2016-06-24 Thread Justin Lemkul 



On 6/24/16 6:23 AM, sun wrote:

Sir
If I do averaging of no. of clusters in case of protein (increased no. of 
clusters as compared to pro-lig complex) at regular intervals of time, It will 
be sufficient to assess if my simulation is converged? In my case clustering in 
addition to secondary structure are conclusive parameters.



Whatever is physically/biologically meaningful for your system.

-Justin



Sent from my iPhone


On 22-Jun-2016, at 7:09 pm, Justin Lemkul  wrote:




On 6/22/16 5:02 AM, sun wrote:
Hello users and experts I have completed a 200 ns protein ligand simulation
using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
change in protein in the presence of ligand and the results are as expected
and correlates to previous references as well. So, shall i believe that
simulation is converged or there is need to do block averaging over time
intervals? If block averaging is required, the parameters like RMSD and
propensities for secondary structure are sufficient to conclude that
simulation is converged? Or could anyone please tell me a suitable procedure
for making blocks and how to average those. With Regards Suniba


Just because a simulation produces expected results does not mean it is 
converged.  You must show that any quantities of interest from which you draw 
your conclusions, are not systematically varying with time.

-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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Re: [gmx-users] Block averaging

2016-06-24 Thread sun 
Sir
If I do averaging of no. of clusters in case of protein (increased no. of 
clusters as compared to pro-lig complex) at regular intervals of time, It will 
be sufficient to assess if my simulation is converged? In my case clustering in 
addition to secondary structure are conclusive parameters. 


Sent from my iPhone

> On 22-Jun-2016, at 7:09 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 6/22/16 5:02 AM, sun wrote:
>> Hello users and experts I have completed a 200 ns protein ligand simulation
>> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
>> change in protein in the presence of ligand and the results are as expected
>> and correlates to previous references as well. So, shall i believe that
>> simulation is converged or there is need to do block averaging over time
>> intervals? If block averaging is required, the parameters like RMSD and
>> propensities for secondary structure are sufficient to conclude that
>> simulation is converged? Or could anyone please tell me a suitable procedure
>> for making blocks and how to average those. With Regards Suniba
> 
> Just because a simulation produces expected results does not mean it is 
> converged.  You must show that any quantities of interest from which you draw 
> your conclusions, are not systematically varying with time.
> 
> -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
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> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Block averaging

2016-06-22 Thread sun 
Allright Sir
Thank you

Sent from my iPhone

> On 22-Jun-2016, at 7:09 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 6/22/16 5:02 AM, sun wrote:
>> Hello users and experts I have completed a 200 ns protein ligand simulation
>> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
>> change in protein in the presence of ligand and the results are as expected
>> and correlates to previous references as well. So, shall i believe that
>> simulation is converged or there is need to do block averaging over time
>> intervals? If block averaging is required, the parameters like RMSD and
>> propensities for secondary structure are sufficient to conclude that
>> simulation is converged? Or could anyone please tell me a suitable procedure
>> for making blocks and how to average those. With Regards Suniba
> 
> Just because a simulation produces expected results does not mean it is 
> converged.  You must show that any quantities of interest from which you draw 
> your conclusions, are not systematically varying with time.
> 
> -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
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> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Block averaging

2016-06-22 Thread Justin Lemkul 



On 6/22/16 5:02 AM, sun wrote:

Hello users and experts I have completed a 200 ns protein ligand simulation
using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
change in protein in the presence of ligand and the results are as expected
and correlates to previous references as well. So, shall i believe that
simulation is converged or there is need to do block averaging over time
intervals? If block averaging is required, the parameters like RMSD and
propensities for secondary structure are sufficient to conclude that
simulation is converged? Or could anyone please tell me a suitable procedure
for making blocks and how to average those. With Regards Suniba



Just because a simulation produces expected results does not mean it is 
converged.  You must show that any quantities of interest from which you draw 
your conclusions, are not systematically varying with time.


-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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[gmx-users] Block averaging

2016-06-22 Thread sun 
Hello users and experts
I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and 
Gromacs v 5.0. I expected to observe a conformational change in protein in the 
presence of ligand and the results are as expected and correlates to previous 
references as well. So, shall i believe that simulation is converged or there 
is need to do block averaging over time intervals? If block averaging is 
required, the parameters like RMSD and propensities for secondary structure are 
sufficient to conclude that simulation is converged? Or could anyone please 
tell me a suitable procedure for making blocks and how to average those. 
With Regards
Suniba

Sent from my iPhone
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