[gmx-users] Issues using Implicit Solvent with Charmm 27

[Juan José Galano Frutos]

Hi there,

I am trying to simulate a protein using a GBSA (implicit solvent) approach,
and first I've been googling a bit in order to set the parameters of the
simulation (mdp file) as better as possible.

I am using the following mdp options for the minimization step (the
parameters of the Implicit Solvent section are also set in the subsequent
NVT and NPT steps):

title   = Energy Minimization   ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp = /lib/cpp  ; Preprocessor

; Define can be used to control processes
define  =
cutoff_scheme   = group

; Parameters describing what to do, when to stop and what to save
integrator  = steep
emtol   = 1.0
emstep  = 0.01
dt  = 0.001
nsteps  = 4
nstenergy   = 500
energygrps  = System

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type = simple
coulombtype = cut-off
rcoulomb= 0
vdwtype = cut-off
rvdw= 0
constraints = none
pbc = no
ld-seed = 1
nstlist = 0
rlist   = 0
comm-mode   = angular
comm-grps   = Protein
optimize_fft= yes

; Implicit solvent

implicit_solvent = GBSA
gb_algorithm = OBC
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
nstgbradii   = 1
rgbradii = 0
gb_epsilon_solvent   = 80
gb_saltconc  = 0
sa_algorithm = ace-approximation
--

The point is that after this minimization step I am obtaining a protein
where the alpha helixes seem to be something relaxed or extended in an
unusual way at least compared to when explicit solvent is used. This fact,
i.e. such a local structural weakening, lead then to a fast protein
unfolding during the subsequent NVT and NPT steps something that I am sure
is not normal that soon.
So, my question is whether there is someone over there has performed
simulations combining CHARMM27 force field and a GBSA approach and has
happened the same? Is there any incompatibility between them using GROMACS?
I could find some papers in which this combination is used but using NAMD.
Any help or advise would be appreciated so much.

Thank you!!


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)
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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

Thank you Justin. The problematic OH is part of the cofactor molecule.
This OH group is located in an extreme part of the cofactor so it
apparently only interacts with solvent, not with the protein.

I'm doing just now some tests of the cofactor solvated in order to
check if the problem comes from the cofactor itself or comes from
other issue.

I'll post here the result of this test whatever it is.

Thank you again.

Best


On 5/16/17 7:03 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I am simulating a protein which include as a cofactor a molecule bearing
*>* some hydroxyl groups. The system is crashing from the begining of the
*>* equilibration step (after the following steps: vaccuum minimization,
*>* solvating, neutralizing, minimization, heating) due to -in all the
*>* replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
*>* degrees.
*>* I checked the structures and the systems looking for either water or
*>* protein parts in so close contact with this hydroxyl groups, but it was not
*>* the case. Then I proceeded to re-minimize again the systems after the
*>* heating step and afterward to relaunch the equilibration step, but again
*>* the same happened. I also checked the topology file of this cofactor but
*>* all seems to be fine, I mean charges.
*>* Then, what could be happening? Is it common this behaviour in hydroxyl
*>* groups?Any help please
*>
What does the problematic OH group interact with?  The over-rotation is a
symptom, not a cause.  If it interacts with your cofactor, the parameters for
that cofactor are likely suspect.  Typical diagnostic steps are in
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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
jalemkul at outerbanks.umaryland.edu
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
(410) 706-7441http://mackerell.umaryland.edu/~jalemkul

==========




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)
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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

For more details, my system also has another cofactor with similar
characteristics (FAD), I mean with hydroxyl groups but all is going fine
with it so far (equilibration step).

As I wrote before I did the following steps:
1- vaccuum minimization
2- solvating
3- neutralizing
4- minimization
5- heating (increases by temperature ramp and using position restraints for
all the components of the system)
6- equilibration (3 sequencial steps: the first step (NVT with a v-rescale
thermostat) is where the system crashes)

here the .mdp file of this first equilibration step:

define  =

integrator  = md
dt = 0.001  ; ps !
nsteps  = 15 ; 150 ps
nstcomm  = 1
nstxtcout  = 1
xtc-precision = 1
nstxout = 0
nstvout = 0
nstfout  = 0
nstlog   = 1
nstenergy  = 1

; Non-bonded Interactions
nstlist   = 10
ns_type= grid
rlist  = 0.9
coulombtype = PME
rcoulomb  = 0.9
vdwtype   = cut-off
rvdw = 0.9
vdw-modifier = Potential-shift-Verlet

; Berendsen temperature coupling is on in two groups
Tcoupl  =  v-rescale
tc-grps =  System
tau_t=  0.1
ref_t =  310

; Energy monitoring
energygrps=  System
DispCorr=  EnerPres

; Isotropic pressure coupling is now off
Pcoupl  =  no
Pcoupltype=  isotropic
tau_p=  5.0
compressibility   =  4.6e-5
ref_p =  1.0

; Generate velocites is off at 310 K
gen_vel  =  no
gen_temp   =  310
gen_seed   =  -1

; Constraints
constraint_algorithm = lincs
lincs_order   = 8
constraints   = all-bonds
lincs-warnangle = 60
disre= simple



Thank you in advance

Best regards

Juan José




2017-05-16 13:03 GMT+02:00 Juan José Galano Frutos <juanj...@gmail.com>:

> Hi there:
>
> I am simulating a protein which include as a cofactor a molecule bearing
> some hydroxyl groups. The system is crashing from the begining of the
> equilibration step (after the following steps: vaccuum minimization,
> solvating, neutralizing, minimization, heating) due to -in all the
> replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
> degrees.
> I checked the structures and the systems looking for either water or
> protein parts in so close contact with this hydroxyl groups, but it was not
> the case. Then I proceeded to re-minimize again the systems after the
> heating step and afterward to relaunch the equilibration step, but again
> the same happened. I also checked the topology file of this cofactor but
> all seems to be fine, I mean charges.
> Then, what could be happening? Is it common this behaviour in hydroxyl
> groups?Any help please
>
> Thanks
>
> 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 <+34%20976%2076%2028%2006>
>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
>
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[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

Hi there:

I am simulating a protein which include as a cofactor a molecule bearing
some hydroxyl groups. The system is crashing from the begining of the
equilibration step (after the following steps: vaccuum minimization,
solvating, neutralizing, minimization, heating) due to -in all the
replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
degrees.
I checked the structures and the systems looking for either water or
protein parts in so close contact with this hydroxyl groups, but it was not
the case. Then I proceeded to re-minimize again the systems after the
heating step and afterward to relaunch the equilibration step, but again
the same happened. I also checked the topology file of this cofactor but
all seems to be fine, I mean charges.
Then, what could be happening? Is it common this behaviour in hydroxyl
groups?Any help please

Thanks

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 
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[gmx-users] Parameterization of FAD (FLAVIN-ADENINE DINUCLEOTIDE)

[Juan José Galano Frutos]

Hi everyone:

Do anyone know where can I find the parameterization files for the FAD
molecule? I've been looking for it online but I've not been able to get it.
I have an ad-hoc method for paremeterize small ligands but I think FAD is
quite common so it should be already well parameterized elsewhere...
Thank you in advance for any 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

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 
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Re: [gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

>
> On 3/27/17 8:42 AM, Juan Jos? Galano Frutos wrote:
> > Hi there,
> >
> > I am trying AFEC simulations in complex (ligand-protein), but sometimes I
> > get the ligands out the binding site, but I dont want that scenary. I was
> > thinking the situation of applying distance retraints between a ligand
> and
> > a protein was already solved in GROMACS version later 5.0... without any
> > necessity of making a hybrid system. But, I'm using version 5.1, and it
> > seems that's not possible doing so, because I'm obtaining errors.
> > Is there currently any happy solution to restraint ligand-protein
> distance?
> > or Has one to still go through the unbrella pulling option to do that?
> >
>
> You need distance as well as orientational restraints.  This is done with
> [intermolecular_interactions], which was a new feature in 5.1.  For
> theory, see
> dx.doi.org/10.1021/ci300505n


>
> -Justin
>

Thank you Justin, very useful help!!!

Juan José

>
> > In the case I need to do a hybrid system what would be a good procedure?
> >
> > Thank you very much.
> >
> >
> > Juan Jos? 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)
> >
>
> --
> ==
>
> 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
>
> ==
>
>
> --
>
> Message: 4
> Date: Mon, 27 Mar 2017 12:57:36 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Regarding Glycine structure
> Message-ID: <1342227d-be3f-89b0-4f44-134a389e6...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/27/17 8:50 AM, Dilip H N wrote:
> > Thanks Justin,
> >
> > But my doubts are..
> > 1] after energy minimization of both glycine non zwitterionic form and
> > zwitterionic form with water, if i visualize it in vmd, the bond between
> > some of the water molecules are broken.. why is this so..??
>
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
>
> What you see on the VMD display is its best guess as to how things are
> connected.  That's not always right.  The topology is always right.
> That's why
> trjconv exists.
>
> > 2] and ran nvt,npt,md simulations respectively...and during analysis
> part i
> > am getting only similar two types of RDF graphs...why is this
> happening...i
> > have made all the indexing, etc., proper...
> >
>
> You have provided no useful information about what these RDF plots are or
> how
> you acquired them, so there's no point for either of us in guessing.
> Maybe the
> distribution(s) that you're looking at simply don't vary as a function of
> protonation state.
>
> > Is there any tutorials for these as an example..?? solving this would
> help
> > me a lot
> >
>
> It's an amino acid in water; it's as easy of a protein system as there is.
> There's nothing special about it that requires a tutorial.
>
> -Justin
>
> >
> >    Sent with Mailtrack
> >  referral=cy16f01.di...@nitk.edu.in=22>
> >
> > On Sun, Mar 26, 2017 at 7:43 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 3/23/17 2:05 PM, Dilip H N wrote:
> >>
> >>> Hello,
> >>>
> >>> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and
> in
> >>> the first step if i do the energy minimization and then visualizes the
> >>> mixture, the glycine is no more in its pure form as before instead it
> has
> >>> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
> >>> bonds with water are also broken. How can i solve these both issues..??
> >>>
> >>>
> >> Glycine didn't convert between forms.  That's impossible; bonds can't
> >> break or form in a molecular mechanical process.  The termini are
> exactly
> >> what you assigned them to be.  If you want them to be something else,
> you
> >> have to assign them as such with pdb2gmx.  Though you should note that
> NH2
> >> and COOH can't coincide at any real pH value.
> >>
> >> -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.
> >> 

[gmx-users] Restraining Protein-ligand distance

[Juan José Galano Frutos]

Hi there,

I am trying AFEC simulations in complex (ligand-protein), but sometimes I
get the ligands out the binding site, but I dont want that scenary. I was
thinking the situation of applying distance retraints between a ligand and
a protein was already solved in GROMACS version later 5.0... without any
necessity of making a hybrid system. But, I'm using version 5.1, and it
seems that's not possible doing so, because I'm obtaining errors.
Is there currently any happy solution to restraint ligand-protein distance?
or Has one to still go through the unbrella pulling option to do that?

In the case I need to do a hybrid system what would be a good procedure?

Thank you very much.


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

[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://thread.gmane.org/gmane.science.biology.gromacs.user/49139,>
*>* http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,
<http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,>
*>* https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g
<https://groups.google.com/forum/#%21topic/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)
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[gmx-users] NORMAL MODES analysis to compute specific heats

[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 <juanj...@gmail.com>
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

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[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

[Juan José Galano Frutos]

On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:
>* Thank you Justin for your replay. I've read that to compute specific
*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool calculates such a correction using the Hessian matrix.
*>* Is for that reason my interest in getting it.
*>* So, my question is why mdrun is not producing the indicated Hessian
*>* matrix as set up in the command line. What I am missing, maybe in the
*>* .mdp file??
*>
And I asked you about the contents of the .mdp file, which you haven't
provided.
  Are you setting "integrator = nm" in it?

-Justin

Sorry Justin. As you can see below I'm using an md integrator. Then,
if I'm understanding well it is possible to obtain the required
Hessian matrix only when you perform normal modes simulations..?

If so, I have another question because although I've been reading a
lot about this quantum correction issue to exactly determine specific
heats I am not yet so clear about this:

What about the printing frequency of energy in this kind of analysis?
Is it really necessary set the higher frequency of printing energy as
possible in order to get good accuracy in this calculation or it is
not certainly so important?

Thanks again for your help.

;
;   juanjo (2016)
;
title   = md_prod
cpp = /lib/cpp
define  =

integrator  = md
dt  = 0.002 ; ps !
nsteps  = 100   ; total 2 ns.
nstcomm = 1
nstxtcout   = 25000 ; each 50 ps.
xtc-precision   = 25000
nstxout = 25000 ; each 50 ps.
nstvout = 25000
nstfout = 25000
nstlog  = 1000
nstenergy   = 1000


 >* Thank
*>>>* On 3/17/17 8:20 AM, Juan José Galano Frutos wrote:
*>>* * Hi there:
*>* *>>* I am trying to calculate the specific heat (Cp) of my
protein, but I should
*>* *>* take into account quantum correction as indicated lately.
Then, I need to
*>* *>* obtain from the production step the Hessian Matrix including the
*>* *>* eigenvectors needed to calculate the vibrational energy.
*>* *>* So, the point is that I set in my script the following order:
*>* *>>* mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
*>* *>* ${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
*>* *>* ${NAME}-hessian.mtx -nice 19 -v
*>* *>>* and in fact, the program apparently recognizes well that a
Hessian matrix
*>* *>* should be printed (see -mtx option below), but however I do
not get such a
*>* *>* Hessian matrix at the end. What's happening here then? I've been looking
*>* *>* for any related discussion online, or whether I have to set
any additional
*>* *>* option, maybe in the mdp file to obtain the Hesssian matrix but I've not
*>* *>* achieved it.
*>* *
*>* What's in your .mdp file?  IIRC the Hessian is only relevant when
doing normal
*>* modes analysis.
*>>* -Justin
*>>>* * Any help, please.
*>* *>>* Thank you very much in advance.
*>* *>>>*  :-)  G  R  O  M  A  C  S  (-:
*>* *>>*  Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*>* *>>* :-)  VERSION 4.6.1  (-:
*>* *>>* Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
*>* *>*Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
*>* *>*  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof,
Christoph Junghans,
*>* *>* Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
*>* *>*Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
*>* *>* Michael Shirts, Alfons Sijbers, Peter Tieleman,
*>* *>>*Berk Hess, David van der Spoel, and Erik Lindahl.
*>* *>>*Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
*>* *>*  Copyright (c) 2001-2012,2013, The GROMACS development team at
*>* *>* Uppsala University & The Royal Institute of Technology, Sweden.
*>* *>* check out http://www.gromacs.org <http://www.gromacs.org>
*>* <http://www.gromacs.org <http://www.gromacs.org>> for more information.
*>* *>>*  This program is free software; you can redistribute it and/or
*>* *>*modify it under the terms of the GNU Lesser General
Public License
*>* *>* as published by the Free Software Foundation; either version 2.1
*>* *>*  of the License, or (at your option) any later version.
*>* *>>*   :-)  mdrun_mpi  (-:
*>* *>>* Option Filename  Type Description
*>* *>* --

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

[Juan José Galano Frutos]

Thank you Justin for your replay. I've read that to compute specific
heats (Cv or Cp) it is necessary calculating quantum correction (using
the tool g_nmeig).
Then, this tool calculates such a correction using the Hessian matrix.
Is for that reason my interest in getting it.
So, my question is why mdrun is not producing the indicated Hessian
matrix as set up in the command line. What I am missing, maybe in the
.mdp file??

Thank


On 3/17/17 8:20 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I am trying to calculate the specific heat (Cp) of my protein, but I should
*>* take into account quantum correction as indicated lately. Then, I need to
*>* obtain from the production step the Hessian Matrix including the
*>* eigenvectors needed to calculate the vibrational energy.
*>* So, the point is that I set in my script the following order:
*>>* mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
*>* ${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
*>* ${NAME}-hessian.mtx -nice 19 -v
*>>* and in fact, the program apparently recognizes well that a Hessian matrix
*>* should be printed (see -mtx option below), but however I do not get such a
*>* Hessian matrix at the end. What's happening here then? I've been looking
*>* for any related discussion online, or whether I have to set any additional
*>* option, maybe in the mdp file to obtain the Hesssian matrix but I've not
*>* achieved it.
*
What's in your .mdp file?  IIRC the Hessian is only relevant when doing normal
modes analysis.

-Justin

>* Any help, please.
*>>* Thank you very much in advance.
*>>>*  :-)  G  R  O  M  A  C  S  (-:
*>>*  Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*>>* :-)  VERSION 4.6.1  (-:
*>>* Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
*>*Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
*>*  Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
*>* Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
*>*Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
*>* Michael Shirts, Alfons Sijbers, Peter Tieleman,
*>>*Berk Hess, David van der Spoel, and Erik Lindahl.
*>>*Copyright (c) 1991-2000, University of Groningen, The Netherlands.
*>*  Copyright (c) 2001-2012,2013, The GROMACS development team at
*>* Uppsala University & The Royal Institute of Technology, Sweden.
*>* check out http://www.gromacs.org
<http://www.gromacs.org> for more information.
*>>*  This program is free software; you can redistribute it and/or
*>*modify it under the terms of the GNU Lesser General Public License
*>* as published by the Free Software Foundation; either version 2.1
*>*  of the License, or (at your option) any later version.
*>>*   :-)  mdrun_mpi  (-:
*>>* Option Filename  Type Description
*>* 
*>*   -s folded-2ns.tpr  InputRun input file: tpr tpb tpa
*>*   -o folded-2ns.trr  Output   Full precision trajectory: trr trj cpt
*>*   -x folded-2ns.xtc  Output, Opt! Compressed trajectory (portable xdr
*>* format)
*>* -cpi  state.cpt  Input, Opt.  Checkpoint file
*>* -cpo  state.cpt  Output, Opt. Checkpoint file
*>*   -c folded-2ns.gro  Output   Structure file: gro g96 pdb etc.
*>*   -e folded-2ns.edr  Output   Energy file
*>*   -g md.log  Output   Log file
*>* -dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
*>* -fieldfield.xvg  Output, Opt. xvgr/xmgr file
*>* -tabletable.xvg  Input, Opt.  xvgr/xmgr file
*>* -tabletftabletf.xvg  Input, Opt.  xvgr/xmgr file
*>* -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
*>* -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
*>* -rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
*>* -tpitpi.xvg  Output, Opt. xvgr/xmgr file
*>* -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
*>*  -eisam.edi  Input, Opt.  ED sampling input
*>*  -eo  edsam.xvg  Output, Opt. xvgr/xmgr file
*>*   -j   wham.gct  Input, Opt.  General coupling stuff
*>*  -jobam.gct  Output, Opt. General coupling stuff
*>* -ffout  gct.xvg  Output, Opt. xvgr/xmgr file
*>* -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
*>* -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
*>*  -px  pullx.xvg  Output, Opt. xvgr/xmgr file
*>*  -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
*>*  -ro   rotation.xvg  Output, Opt. xvgr/xmgr file
*>*  -ra  rotangles.log  Output, Opt. Log file
*>*  -rs   rotslabs.lo

[gmx-users] MDRUN doesn't print Hessian Matrix as ordered.

[Juan José Galano Frutos]

Hi there:

I am trying to calculate the specific heat (Cp) of my protein, but I should
take into account quantum correction as indicated lately. Then, I need to
obtain from the production step the Hessian Matrix including the
eigenvectors needed to calculate the vibrational energy.
So, the point is that I set in my script the following order:

mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
${NAME}-hessian.mtx -nice 19 -v

and in fact, the program apparently recognizes well that a Hessian matrix
should be printed (see -mtx option below), but however I do not get such a
Hessian matrix at the end. What's happening here then? I've been looking
for any related discussion online, or whether I have to set any additional
option, maybe in the mdp file to obtain the Hesssian matrix but I've not
achieved it.
Any help, please.

Thank you very much in advance.


 :-)  G  R  O  M  A  C  S  (-:

 Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

:-)  VERSION 4.6.1  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.

  :-)  mdrun_mpi  (-:

Option Filename  Type Description

  -s folded-2ns.tpr  InputRun input file: tpr tpb tpa
  -o folded-2ns.trr  Output   Full precision trajectory: trr trj cpt
  -x folded-2ns.xtc  Output, Opt! Compressed trajectory (portable xdr
format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -c folded-2ns.gro  Output   Structure file: gro g96 pdb etc.
  -e folded-2ns.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tabletftabletf.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eo  edsam.xvg  Output, Opt. xvgr/xmgr file
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
 -ro   rotation.xvg  Output, Opt. xvgr/xmgr file
 -ra  rotangles.log  Output, Opt. Log file
 -rs   rotslabs.log  Output, Opt. Log file
 -rt  rottorque.log  Output, Opt. Log file
-mtx folded-hessian.mtx  Output, Opt! Hessian matrix  <<<
 -dn dipole.ndx  Output, Opt. Index file
-multidirrundir  Input, Opt., Mult. Run directory
-membed  membed.dat  Input, Opt.  Generic data file
 -mp membed.top  Input, Opt.  Topology file
 -mn membed.ndx  Input, Opt.  Index file



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)
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[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Juan José Galano Frutos]

Thanks Mark for your replay.

About the part where you say...

>The problem comes when one side of your shell can see
>the other across the gap within the cutoff, and you're still thinking of it
>as an isolated single shell

...yes, I agree with you that one must be aware about this issue. But about
the other aspect you pointed out:

>or if you're using PME, so that everything
>sees everything at long range

...I'm not so clear.

The point is we've used PME both in the original simulations and in the 'rerun'
ones (the .mdp files are almost idem). Then, what should we do here to
avoid this
problem? ...maybe to turn off the PME long-range electrostatics only
in the rerun
step? If so, wouldn't that importantly change results in terms of
Energy only by
the effect of changing the electrostatic treatment?
Another solution? ...maybe setting up a different electrostatics from
the begining
(the same both in the original simulations and in the rerun ones)?
What's treatment
we could use to get the longe-range electrostatics turned off without
loosing so
much accuracy in terms of Energy? ...'cut-off', 'PME-Switch' maybe? ... or a
coulomb-modifier such as Potential-shift-Verlet?

Any suggestion there, please?

Thanks a lot.


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-February/111037.html

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 
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[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Juan José Galano Frutos]

Hi there,

We are doing simulation in which we are interested in studying Energies,
Enthalpies, etc. changes in systems with increasingly water shells around a
protein. In this sense, we first extract bulk waters in order to leave the
mentioned water shells with a defined radius around the protein. Then we do
a rerun in order to recalculate the system energies, but my doubt here is:
what exactly to do with PBC in the .mdp file? My doubts here come up
because the system now (protein + water shell) is not a geometric box like
a dodecahedron or a cubic box, and I am afraid about whether the energies I
am obtaining are totally wrong. Do you think it will be better here not to
use PBC or you think there is no matter in doing the rerun keeping PBC on?
I guess that keeping PBC on, there will be some empty space between each
side box (the space left by water removed), so I feel it could be important
...

Thank you very much.


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

[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

[Juan José Galano Frutos]

Thank you Mark:

That's a pitty!! I am not an informatician, is for that that I am not
trying to implement it, becasue probably I do it not through a good or
efficient code.
Anyway I've been able to solve my problem using g_select and make_ndx and
and very iterative bash scripts on each frame of my trajectories and then
paste them again in a new one with trjcat.
Finally mdrun -rerun on the new trr and g_energy et Voîla!!!

Thank you again Mark, hopefully someone with good programming skills want
to develop this functionality in trjorder on ahead. It would be really
useful!!!


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)
-- 
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[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

[Juan José Galano Frutos]

Hi there:

I am trying to analyze a water shell around a protein, and we are studing
for instance deltaH in some molecular processes. In this sense as you know
Enthalpies not only depend on Potential energy but also on Kinetic energies
and a term pV, so that it is crutial having velocities for calculating
Kinetic energies. As far as I know the only tool exists to order and
extract by for instance a distance criterium a water shell around a protein
is TRJORDER, however this program not print out the velocities in the
output trajectories so it is impossible to obtain the Enthalpies in my
anallysis.

Could you suggest to me any solutions...
Wouldn't be useful to add that functionality to TRJORDER program? Would it
be?

Thank you very much in advance.


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!

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

[gmx-users] Enthalpy and energy questions on a solvated protein

[Juan José Galano Frutos]

Hi dear all:

I'm trying to obtain the deltaH (enthalpy = potential energy + pV) in a
given molecular process, so for that I'm drawing the enthalpy values of my
systems (a small protein conveniently solvated and neutralized) from using
gmx_energy on the .edr files.

Then, my questions and reflexions are:
Are the enthalpy or energy values I'm here obtaining actually reliable in
terms of experimental real values taking into account I'm using the pretty
rigorous CHARMM27 force field??

My doubts here come up given that I'm obtaining values for my systems in a
10 to the 6 kJ/mol order (e.g -1 155 621 kJ/mol), which seems to me
excessively high.

I know, of course, these enthalpy or energy values strongly depend on the
amount of solvent you have in your system, and I have done some tests in
order to verify how is the variation of these energies in relation with the
number of water molecules solvating my protein.
But, what I wouldn't expect here is that such energy and enthalpy values
were varied in about a 10 to 4 or 10 to the 5 order in simulation replicas
carried out on my solvated protein. See the following data:
replica Ave Enthalpy (kJ/mol)
1  -1161980
2  -1142910
3  -1217530

Believe you that these significant changes are a normal variation of these
energies in my simulations taking into account the system is exactly the
same (just gen_seed in the velocity options was different)??

Any suggestion to obtain reliable enthalpy values in the event the results
I'm getting are really senseless???

Thanks a lot.



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

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