[gmx-users] MSD close to a surface/layer

[Tuanan Lourenço]

Hi everyone,
I have a simulation with a metal slab and I would like to get the MSD of
the molecules close to the slab. I have tried the gmx selection that works
pretty well to structural analysis, but to the dynamical analysis such as
msd or rotacf there are some issues. I have tried the dynan_mol_com flag in
the gmx selection. But it is writing a huge index file, in which each group
index is the number of the molecules close to the slab in a specific frame.
I would like to know if it is possible to put a restriction in the gmx msd
and get the MSD in a specific box region.
Thanks

-- 
__
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE 
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[gmx-users] MSD close to a surface/slab

[Tuanan Lourenço]

Hi everyone,
I have a simulation with a metal slab and I would like to get the MSD of
the molecules close to the slab. I have tried the gmx selection that works
pretty well to structural analysis, but to the dynamical analysis such as
msd or rotacf there are some issues. I have tried the dynan_mol_com flag in
the gmx selection. But it is writing a huge index file, in which each group
index is the number of the molecules close to the slab in a specific frame.
I would like to know if it is possible to put a restriction in the gmx msd
and get the MSD in a specific box region.
Thanks


-- 
__
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE 
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[gmx-users] RV: Running simulation differences

[Gonzalez Fernandez, Cristina]

Hi Justin,


Sorry for the misunderstanding. I am simulating the interaction of a lipid with 
water. I obtain practically the same value for the coulomb interaction energy, 
but I am not able to get a value for the van der waals energy close to the 
published one (although I have used the same settings than the ones used in the 
article). Therefore, I checked tha GMX manual and I tried to modified the 
settings that affect the van der waals energy in order to get a better value: 
vdwtype, vdw-modifier, rvdw and DispCorr (as I am using GROMOS96 FF I don't 
consider rvdw-switch).


This is the .mdp file:


title= Lipid A  simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps= 550; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 5000; save coordinates every 1.0 ps
nstvout = 5000; save velocities every 1.0 ps
nstenergy   = 5000; save energies every 1.0 ps
nstlog= 5000; update log file every 1.0 ps
nstxtcout   = 5000
xtc-grps= System
; Bond parameters
continuation= yes; restarting after NVT
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Nonbonded settings
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 5; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.4; short-range electrostatic cutoff (in nm)
rvdw= 1.4; short-range van der Waals cutoff (in nm)
rlist   = 1.41
vdwtype = Cut-off
vdw_modifier= None
verlet-buffer-drift = -1
; Electrostatics
coulombtype= Reaction-Field; Particle Mesh Ewald for long-range 
electrostatics
epsilon_rf  = 61
; Temperature coupling is on
tcoupl   = nose-hoover; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.2   ; time constant, in ps
ref_t= 298; reference temperature, one for each 
group, in K
; Pressure coupling is oN
pcoupl  = Parrinello-Rahman ; Pressure coupling on in 
NPT
pcoupltype  = isotropic ; uniform scaling of box 
vectors
tau_p   = 0.5   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal 
compressibility of water, bar^-1
;refcoord_scaling= com
; Periodic boundary conditions
pbc= xyz; 3-D PBC
;Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; assign velocities from Maxwell 
distribution
;gen_temp= 278; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed

I would greatly appreciate if you could help me, because I don't know what else 
I can do,

C.




De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: jueves, 20 de diciembre de 2018 19:52:20
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Running simulation differences

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:

> Hi Justin,
>
>
> Do you think that the difference between a value of -280 ± 37 kj/mol
> obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?
>
>
As I said before, no, a massive difference like that, outside the error
bars, is not acceptable.

If you want more useful advice, you'll have to tell us exactly what you're
doing and trying to compare.

-Justin


>
> Thank you so much for all your help
>
> C.
>
> 
> De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin
> Lemkul 
> Enviado: martes, 18 de diciembre de 2018 15:34:07
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Running simulation differences
>
> On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
> cristina.gonzalezf...@unican.es> wrote:
>
> > Hi again Justin,
> >
> > I've been thinking about the normal variability between MD simulations
> you
> > commented. I am simulating the interaction of a lipid with water, but the
> > van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> > is considerably different from the 

Re: [gmx-users] Running simulation differences

[Gonzalez Fernandez, Cristina]

Hi Justin,


Sorry for the misunderstanding. I am simulating the interaction of a lipid with 
water. I obtain practically the same value for the coulomb interaction energy, 
but I am not able to get a value for the van der waals energy close to the 
published one (although I have used the same settings than the ones used in the 
article). Therefore, I checked tha GMX manual and I tried to modified the 
settings that affect the van der waals energy in order to get a better value: 
vdwtype, vdw-modifier, rvdw and DispCorr (as I am using GROMOS96 FF I don't 
consider rvdw-switch).


This is the .mdp file:


title= Lipid A  simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps= 550; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 5000; save coordinates every 1.0 ps
nstvout = 5000; save velocities every 1.0 ps
nstenergy   = 5000; save energies every 1.0 ps
nstlog= 5000; update log file every 1.0 ps
nstxtcout   = 5000
xtc-grps= System
; Bond parameters
continuation= yes; restarting after NVT
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Nonbonded settings
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 5; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.4; short-range electrostatic cutoff (in nm)
rvdw= 1.4; short-range van der Waals cutoff (in nm)
rlist   = 1.41
vdwtype = Cut-off
vdw_modifier= None
verlet-buffer-drift = -1
; Electrostatics
coulombtype= Reaction-Field; Particle Mesh Ewald for long-range 
electrostatics
epsilon_rf  = 61
; Temperature coupling is on
tcoupl   = nose-hoover; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.2   ; time constant, in ps
ref_t= 298; reference temperature, one for each 
group, in K
; Pressure coupling is oN
pcoupl  = Parrinello-Rahman ; Pressure coupling on in 
NPT
pcoupltype  = isotropic ; uniform scaling of box 
vectors
tau_p   = 0.5   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal 
compressibility of water, bar^-1
;refcoord_scaling= com
; Periodic boundary conditions
pbc= xyz; 3-D PBC
;Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; assign velocities from Maxwell 
distribution
;gen_temp= 278; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed

I would greatly appreciate if you could help me, because I don't know what else 
I can do,

C.




De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: jueves, 20 de diciembre de 2018 19:52:20
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Running simulation differences

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:

> Hi Justin,
>
>
> Do you think that the difference between a value of -280 ± 37 kj/mol
> obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?
>
>
As I said before, no, a massive difference like that, outside the error
bars, is not acceptable.

If you want more useful advice, you'll have to tell us exactly what you're
doing and trying to compare.

-Justin


>
> Thank you so much for all your help
>
> C.
>
> 
> De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin
> Lemkul 
> Enviado: martes, 18 de diciembre de 2018 15:34:07
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Running simulation differences
>
> On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
> cristina.gonzalezf...@unican.es> wrote:
>
> > Hi again Justin,
> >
> > I've been thinking about the normal variability between MD simulations
> you
> > commented. I am simulating the interaction of a lipid with water, but the
> > van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> > is considerably different from the 

Re: [gmx-users] duplicated position restraint statements

[Alex]

That is way too much effort for not simply fixing the bug in the restraint
generator, I hoped someone would just know off the top of their head ;)

On Thu, Dec 20, 2018, 12:20 PM Justin Lemkul  On Thu, Dec 20, 2018 at 2:08 PM Alex  wrote:
>
> > Anyone? :)
> >
> >
> Calculate a single-point energy on a given configuration with and without
> duplicates. If the energy differs, you have your answer.
>
> -Justin
>
>
> >
> > On 12/16/2018 2:54 AM, Alex wrote:
> > > Hi all,
> > >
> > > Quick question: in some of our models, the list of position restraints
> > > as part of the permanent topology is created externally, based on the
> > > atomic positions. Unfortunately, there is a slight bug in the
> > > restraint generator and for a small portion of the restrained atoms
> > > the statements are duplicated, i.e. there can be two identical
> > > statements for something like four atoms out of ~200. Does grompp
> > > interpret a duplicate as restraint with twice the force constants, is
> > > it ignored? In other words, are duplicates additive?
> > >
> > > Thanks,
> > >
> > > 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.
> >
>
>
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==
> --
> 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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Re: [gmx-users] duplicated position restraint statements

[Justin Lemkul]

On Thu, Dec 20, 2018 at 2:08 PM Alex  wrote:

> Anyone? :)
>
>
Calculate a single-point energy on a given configuration with and without
duplicates. If the energy differs, you have your answer.

-Justin


>
> On 12/16/2018 2:54 AM, Alex wrote:
> > Hi all,
> >
> > Quick question: in some of our models, the list of position restraints
> > as part of the permanent topology is created externally, based on the
> > atomic positions. Unfortunately, there is a slight bug in the
> > restraint generator and for a small portion of the restrained atoms
> > the statements are duplicated, i.e. there can be two identical
> > statements for something like four atoms out of ~200. Does grompp
> > interpret a duplicate as restraint with twice the force constants, is
> > it ignored? In other words, are duplicates additive?
> >
> > Thanks,
> >
> > 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
>
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> 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.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
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[gmx-users] Position restraints while performing pulling run for Umbrella sampling

[ARNAB MUKHERJEE]

Hi,

I am intending to perform pulling run for umbrella sampling, on my coarse
grained DNA protein system where I have a bundle containing 20 DNAs and
proteins. I want to pull 1 DNA out of this bundle to perform Umbrella
Sampling. I was going through this tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
So since I want to pull 1 DNA out of the bundle, I would like to position
restrain the atoms of the other 19 DNAs. But as mentioned here
http://www.gromacs.org/Documentation/How-tos/Position_Restraints, I need to
add the position restraints under the molecule type of DNA, in my .top
file, but then shouldn't it restrain the atoms of all the 20 DNAs? How can
I restrain the atoms of other 19 DNAs, except the DNA that I am pulling?

I would highly appreciate any help.

Thank you very much,

Regards,

Arnab
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Re: [gmx-users] duplicated position restraint statements

[Alex]

Anyone? :)


On 12/16/2018 2:54 AM, Alex wrote:

Hi all,

Quick question: in some of our models, the list of position restraints 
as part of the permanent topology is created externally, based on the 
atomic positions. Unfortunately, there is a slight bug in the 
restraint generator and for a small portion of the restrained atoms 
the statements are duplicated, i.e. there can be two identical 
statements for something like four atoms out of ~200. Does grompp 
interpret a duplicate as restraint with twice the force constants, is 
it ignored? In other words, are duplicates additive?


Thanks,

Alex


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Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Justin Lemkul]

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear Sir,
>
> Thanks a lot for the inputs. I tried incorporating the forcefield
> parameters (directory) obtained from the atbserver in the working
> directory. When i was trying to convert the protein.pdb to .gro, I noticed
> that the forcefield showed up in the menu as one included in local
> directory, just as it does for cgenff in the tutorial.
> I chose it to prepare the protein.gro file and then incorporated the
> jz4.itp into the topology file of protein.
> I was able to overcome the issues and complete npt and nvt equilibration.
> Will proceed with the mdrun tomorrow morning.
> Can you please suggest a solution for resuming the mdrun, in case there is
> an interruption in the connectivity with the server. As i am running the
> simulation from a laptop, I might not be able to leave it on through out.
>

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

Checkpointing makes continuing a simulation seamless.

-Justin

-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
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Re: [gmx-users] Running simulation differences

[Justin Lemkul]

On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:

> Hi Justin,
>
>
> Do you think that the difference between a value of -280 ± 37 kj/mol
> obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?
>
>
As I said before, no, a massive difference like that, outside the error
bars, is not acceptable.

If you want more useful advice, you'll have to tell us exactly what you're
doing and trying to compare.

-Justin


>
> Thank you so much for all your help
>
> C.
>
> 
> De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin
> Lemkul 
> Enviado: martes, 18 de diciembre de 2018 15:34:07
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Running simulation differences
>
> On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
> cristina.gonzalezf...@unican.es> wrote:
>
> > Hi again Justin,
> >
> > I've been thinking about the normal variability between MD simulations
> you
> > commented. I am simulating the interaction of a lipid with water, but the
> > van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> > is considerably different from the published value (-361 kj/mol).
> However,
> > according to your email maybe these values can be considered similar. Do
> > you think my value and the published one are similar? How can I reduced
> the
> > error of the results because my value correspond to a long
>
>
> I would not call those values similar at all. The two quantities you posted
> before were within error of one another; those are similar. A difference of
> over 100 kJ/mol, outside error, is enormous. You need to evaluate what
> you're doing because in that case, I suspect something is inconsistent
> between what is published and what you're doing.
>
>
> > simulation (60 ns)? Could you recommend me a paper where is stated the
> > common deviations/errors that are acceptable to a simulation result?
> >
>
> There is none to my knowledge, and certainly can't be generalized.
> Different quantities have different tolerances. Different software may
> produce somewhat different results, as well.
>
> Also I wouldn't consider 60 ns long, by any means :)
>
> -Justin
>
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>


-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
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Re: [gmx-users] Running simulation differences

[Gonzalez Fernandez, Cristina]

Hi Justin,


Do you think that the difference between a value of -280 ± 37 kj/mol obtained 
by Gromacs and -367 kj/mol obtained by NAMD can be acceptable?


Thank you so much for all your help

C.


De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: martes, 18 de diciembre de 2018 15:34:07
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] Running simulation differences

On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:

> Hi again Justin,
>
> I've been thinking about the normal variability between MD simulations you
> commented. I am simulating the interaction of a lipid with water, but the
> van der waals energy value that I obtain (-257.25  ± 35.86 kj/mol) for me
> is considerably different from the published value (-361 kj/mol). However,
> according to your email maybe these values can be considered similar. Do
> you think my value and the published one are similar? How can I reduced the
> error of the results because my value correspond to a long


I would not call those values similar at all. The two quantities you posted
before were within error of one another; those are similar. A difference of
over 100 kJ/mol, outside error, is enormous. You need to evaluate what
you're doing because in that case, I suspect something is inconsistent
between what is published and what you're doing.


> simulation (60 ns)? Could you recommend me a paper where is stated the
> common deviations/errors that are acceptable to a simulation result?
>

There is none to my knowledge, and certainly can't be generalized.
Different quantities have different tolerances. Different software may
produce somewhat different results, as well.

Also I wouldn't consider 60 ns long, by any means :)

-Justin

--

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==
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Re: [gmx-users] Protein-ligand complex simulation and ATBserver file

[Prasanth G, Research Scholar]

Dear Sir,

Thanks a lot for the inputs. I tried incorporating the forcefield
parameters (directory) obtained from the atbserver in the working
directory. When i was trying to convert the protein.pdb to .gro, I noticed
that the forcefield showed up in the menu as one included in local
directory, just as it does for cgenff in the tutorial.
I chose it to prepare the protein.gro file and then incorporated the
jz4.itp into the topology file of protein.
I was able to overcome the issues and complete npt and nvt equilibration.
Will proceed with the mdrun tomorrow morning.
Can you please suggest a solution for resuming the mdrun, in case there is
an interruption in the connectivity with the server. As i am running the
simulation from a laptop, I might not be able to leave it on through out.
Thank you once again.

---
Your #include statements are out of order. The #include statement for the
parent force field (the line above) should appear before anything else in
the topology, as it defines the atom types. The ffnonbonded.itp file does,
in fact, define CAro, which is a nonstandard type from ATB. I also suspect
that your specified PATH is lacking an initial / - note that full PATH
information is not necessary if the force field subdirectory is in $GMXLIB
or in the working directory.

-Justin

-- 

==

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com


==

On Wed, Dec 19, 2018 at 3:05 PM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "jz4.itp"
>
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
>
> ; Include topology for ions
> #include "home/bio1/PG/gromos54a7_atb.ff/ions.itp"
>
> ; Include water topology
> #include "home/bio1/PG/gromos54a7_atb.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> [ system ]
> ; Name
> LYSOZYME
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> JZ4 1
> 
> However, when i try to execute the grompp to add ions, the error still
> persists-
>
> *Fatal error:*
>
> *Atomtype CAro not found *
>
> Could you please tell me, if i have to change the way this  has to be
> done. Here is the list of parameter files obtained from the ATBserver.
> link- https://atb.uq.edu.au/molecule.py?molid=342699#panel-md
> ---
> aminoacids.c.tdb, aminoacids.hbd, amonoacids.n.tbb, aminoacids.r2b,
> aminoacids.rtp, aminoacids.vsd, atomtypes.atp, dppc.itp, ffbonded.itp,
> ffdum.itp, ffnonbonded.itp, forcefield.doc, forcefield.itp, ions.itp,
> popc.itp, README.md, spc.itp, spce.itp, tip3.itp, tip4.itp, tmcl.itp,
> watermodels.dat
> ---
>
> Thanks in advance,
> Prasanth.
>
> 
> Are you trying to combine this ligand topology with the CHARMM protein
> topology generated in the tutorial? If so, that's fundamentally incorrect
> and you can never make that work.
>
> If you're doing things entirely within the context of GROMOS, then you
> likely need additional files from the ATB server that provide parameters
> for the "unknown" atom types.
>
> -Justin
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==
>
>
> --
>
> On Tue, Dec 18, 2018 at 10:49 AM Sri Prasanth Ghanta, Doctoral Research
> Scholar, Biosciences, SSSIHL  wrote:
>
>> Dear all,
>>
>> I have started following the new tutorial
>>  and the old tutorial
>> 
>> to carryout the simulation of JZ4 with Lysozyme.
>> I was unable to run the cgenff script as I am not aware of setting up
>> microenvironment in Ubuntu to run older python version, which is essential