[gmx-users] NORMAL MODES analysis to compute specific heats

2017-03-21 Thread Juan José Galano Frutos 
On 3/20/17 9:34 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I've been googled a bit about this issue (
*>* http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,

*>* http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,

*>* https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g
),
but
*>* I've not found answers to my doubts yet.
*>>* My situation is that I want to obtain specific heats (Cp) of my systems
*>* (protein solvated and neutralized) but, of course, at the Temperature and
*>* Pressure of my experiments. So, my idea here is carry out a Normal Modes
*>* analysis to extract the Hessian matrix but at least after the equilibration
*>* step of my system. I'm interested in doing it so because Cp values only
*>* make sense in relation with Temperature.
*>* My doubts come up, however, when I read through the posted discussion and I
*>* find that NM analyses apparently should be performed after minimization
*>* steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
*>* that is really so or if it is possible carry out this calculation after,
*>* for instance, an equilibration or a productive step in which, of course,
*>* some previous minimizations have already been performed as usual?
*>>* I've not understood also the suggestion made in one of the above referenced
*>* discussions in which David Van der Spoel recommended set all cut-offs to
*>* zero (=infinite), see below:
*>>>* You can use the g96 coordinate format instead of using the trr file
*>>* from the conjugate gradients energy minimization.
*>>* Set all cut-offs to zero (= infinite).
*>>* What's the reason for that?
*>* Where one should set to zero the cut-offs...? Just in the NM step or
*>* that is for the minimization steps?
*>
>NMA requires that you be in an energy minimum (and hence the requirement for
>exhaustive energy minimization, well below what is normally considered adequate
>for a standard MD simulation), is typically done in vacuo (hence "infinite"
>cutoffs/no PBC) and is only valid if the fundamental modes of motion are
>harmonic.  At elevated temperature (anything non-0 K) you have anharmonicity in
>many motions and the harmonic approximation fails.

>-Justin

Ok, now I'm more clear. Thank you very much Justin.

Best.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
-- 
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] NORMAL MODES analysis to compute specific heats

2017-03-21 Thread Justin Lemkul 



On 3/20/17 9:34 AM, Juan José Galano Frutos wrote:

Hi there:

I've been googled a bit about this issue (
http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,
https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but
I've not found answers to my doubts yet.

My situation is that I want to obtain specific heats (Cp) of my systems
(protein solvated and neutralized) but, of course, at the Temperature and
Pressure of my experiments. So, my idea here is carry out a Normal Modes
analysis to extract the Hessian matrix but at least after the equilibration
step of my system. I'm interested in doing it so because Cp values only
make sense in relation with Temperature.
My doubts come up, however, when I read through the posted discussion and I
find that NM analyses apparently should be performed after minimization
steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
that is really so or if it is possible carry out this calculation after,
for instance, an equilibration or a productive step in which, of course,
some previous minimizations have already been performed as usual?

I've not understood also the suggestion made in one of the above referenced
discussions in which David Van der Spoel recommended set all cut-offs to
zero (=infinite), see below:


You can use the g96 coordinate format instead of using the trr file
from the conjugate gradients energy minimization.
Set all cut-offs to zero (= infinite).


What's the reason for that?
Where one should set to zero the cut-offs...? Just in the NM step or
that is for the minimization steps?



NMA requires that you be in an energy minimum (and hence the requirement for 
exhaustive energy minimization, well below what is normally considered adequate 
for a standard MD simulation), is typically done in vacuo (hence "infinite" 
cutoffs/no PBC) and is only valid if the fundamental modes of motion are 
harmonic.  At elevated temperature (anything non-0 K) you have anharmonicity in 
many motions and the harmonic approximation fails.


-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.

[gmx-users] NORMAL MODES analysis to compute specific heats

2017-03-21 Thread Juan José Galano Frutos 
Sorry for insisting, but has no-one any idea of this?

Thanks

Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)

-- Forwarded message --
From: Juan José Galano Frutos 
Date: 2017-03-20 14:34 GMT+01:00
Subject: NORMAL MODES analysis to compute specific heats
To: gmx-us...@gromacs.org


Hi there:

I've been googled a bit about this issue (http://thread.gmane.org/
gmane.science.biology.gromacs.user/49139, http://www.gromacs.org/
Documentation/How-tos/Normal_Mode_Analysis, https://groups.google.com/
forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but I've not found answers to
my doubts yet.

My situation is that I want to obtain specific heats (Cp) of my systems
(protein solvated and neutralized) but, of course, at the Temperature and
Pressure of my experiments. So, my idea here is carry out a Normal Modes
analysis to extract the Hessian matrix but at least after the equilibration
step of my system. I'm interested in doing it so because Cp values only
make sense in relation with Temperature.
My doubts come up, however, when I read through the posted discussion and I
find that NM analyses apparently should be performed after minimization
steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
that is really so or if it is possible carry out this calculation after,
for instance, an equilibration or a productive step in which, of course,
some previous minimizations have already been performed as usual?

I've not understood also the suggestion made in one of the above referenced
discussions in which David Van der Spoel recommended set all cut-offs to
zero (=infinite), see below:

> You can use the g96 coordinate format instead of using the trr file
> from the conjugate gradients energy minimization.
> Set all cut-offs to zero (= infinite).

What's the reason for that?
Where one should set to zero the cut-offs...? Just in the NM step or
that is for the minimization steps?

Thank you very much for your help.



Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06 <+34%20976%2076%2028%2006>

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
-- 
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.