Re: [gmx-users] Gromacs 2018.3 Exceeding Memory Issue

[Mark Abraham]

Hi,

On Tue, Nov 27, 2018 at 4:31 AM Peiyin Lee  wrote:

> Hi, all GROMACS users,
>
>I am trying to run jobs with Gromacs 2018.3 version and constantly got a
> memory exceeding error. The system I ran is an all-atom system with 21073
> atoms. The largest file that is estimated to be generated is around 5.8 GB.
>

Estimate sizes of disk files don't matter here.


> My jobs got constantly killed after running for only around 15 minutes and
> got an error message like this: "slurmstepd: error: Job 12381762 exceeded
> memory limit (123122052 > 12288), being killed". I have tried using a
>

128MB is pretty tiny these days - no compute node will have less than 1GB
physical memory, so I suggest to ask for that.

GROMACS should never leak memory as the simulation progresses - if you
think you are seeing that (e.g. with slightly larger memory limit, slurm
interrupts a bit later) then we would like to see a bug report at
https://redmine.gromacs.org


> larger memory specification (12GB/core) but it would take too long to wait
> and I don't think my job really uses that many memories. I have attached my
> .mdp file as below:
> "title = NVT Production Run for Trpzip4 in pure H2O
>
> define =; position restrain the protein
>
> ; Run parameters
>
> integrator = md ; leap-frog integrator
>
> nsteps = 5000 ; 0.002 * 5 = 10 ps (100 ns)
>
> dt = 0.002 ; 2 fs
>
> ; Output control
>
> nstenergy = 1 ; save energies every 20 ps
>
> nstlog = 1 ; update log file every 20 ps
>
> nstxout-compressed = 1  ; 20ps
>
> compressed-x-precision = 200   ; 0.05
>
> compressed-x-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
>
> ; Neighborsearching
>
> ns_type = grid ; search neighboring grid cels
>
> nstlist = 5 ; 10 fs
>
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
>
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>
> ; Electrostatics
>
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
>
> pme_order = 4 ; cubic interpolation
>
> fourierspacing = 0.16 ; grid spacing for FFT
>
> ; Temperature coupling is on
>
> tcoupl = V-rescale ; More accurate thermostat
>
> tc-grps = Protein SOL NA; 2 coupling groups - more accurate
>

Off topic, but it is not good practice to couple ions separately. Did you
perhaps follow some tutorial that we can ask the author to fix?


> tau_t = 0.5 0.5 0.5; time constant, in ps
>
> ref_t = 400 400  400 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is on
>
> pcoupl = No  ; Pressure coupling on in NPT
>
> pcoupltype = isotropic ; uniform scaling of x-y box vectors,
> independent z
>
> tau_p = 5.0 ; time constant, in ps
>
> ref_p = 1.0 ; reference pressure, x-y, z (in bar)
>
> compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
>
> ; Periodic boundary conditions
>
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = no ; Velocity generation is off"
> and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
> -noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo md.cpt
> -g md.log".


Looks fine. I encourage everybody to use the default file names, and
organize their projects into natural groups for the infrastructure, like
directories. Renaming them doesn't add value and makes your life more
complicated when you're doing restarts.

Mark


> This is my first time posting so please excuse anything that's
> unclear. I will try to clarify if needed. Any help is greatly appreciated!
>
> Regards,
> Peiyin Lee
> --
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Re: [gmx-users] preparing input file for GPU

[Mark Abraham]

Hi,

You just need to not choose such groups. See
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#output-control

Mark

On Tue, Nov 27, 2018 at 7:10 AM Seketoulie Keretsu 
wrote:

> I am running a protein ligand simulation for the first time after
> installation of GPU. When i execute mdrun i got this message,
> "Multiple energy groups is not implemented for GPUs, falling back to
> the CPU. ". I understand i have to remove the energy group in the .mdp
> file. But I am not sure how to do that. What are the changes i should
> do to make it compatible for GPU execution? Kindly suggest me a
> material or link where i can find the information. I have looked at
> some gromacs manual but could not really find for the specific
> problem. Suggestions on where to look will be appreciated too.
>
> Here is my .mdp file:
> title   = Protein-ligand complex MD simulation
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 10; 2 * 10 = 200 ps (0.2 ns)
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 0 ; suppress .trr output
> nstvout = 0 ; suppress .trr output
> nstenergy   = 5000  ; save energies every 10.0 ps
> nstlog  = 5000  ; update log file every 10.0 ps
> nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps
> compressed-x-grps   = System
> energygrps  = Protein UNK
> ; Bond parameters
> continuation= yes   ; first dynamics run
> 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
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10; 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)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein_UNK  Water_and_ions; two coupling groups -
> more accurate
> tau_t   = 0.1   0.1 ; time constant, in ps
> ref_t   = 300   300 ; reference temperature,
> one for each group, in K
> ; Pressure coupling
> pcoupl  = Parrinello-Rahman ; pressure coupling is on for
> NPT
> pcoupltype  = isotropic ; uniform scaling of box
> vectors
> tau_p   = 2.0   ; time constant, in ps
> ref_p   = 1.0   ; reference pressure, in bar
> compressibility = 4.5e-5; isothermal
> compressibility of water, bar^-1
> ; 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
> x   x
> xxx
> x   x
> xxx
> Thanking you in anticipation.
>
> Seke
> --
> Gromacs Users mailing list
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 95

[Seketoulie Keretsu]

Dear Alex

Thank you for the "shameless self promotion".  Have been looking for
some classic gromacs products lately. Have seen some interesting
methods in area of protein-ligand interactions. If you have some  new
and interesting gromacs papers related to Protein-ligand studies
please suggest it here.

Also came across this paper out of Stanford university. 400 micro sec
simulations. Just blown my mind.
https://www.nature.com/articles/s41467-016-0015-8

Will really appreciate if you can suggest .

Appreciate you guys for all the help so far.

Best, Seke
On Tue, Nov 27, 2018 at 1:05 PM
 wrote:
>
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Parameterizing N-terminal capping (Raji)
>2. Re: Distance calculation (rose rahmani)
>3. Re: Interaction energy (Mark Abraham)
>4. shameless self-promotion (Alex)
>5. Gromacs 2018.3 Exceeding Memory Issue (Peiyin Lee)
>6. Re: Charge system simulation problem (Karpurmanjari Kakati)
>
>
> --
>
> Message: 1
> Date: Mon, 26 Nov 2018 12:50:05 -0600
> From: Raji 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Parameterizing N-terminal capping
> Message-ID:
> 
> Content-Type: text/plain; charset="utf-8"
>
> Hi
>
> I am trying to parameterize the N-terminal ?carboxybenzyl? capping for
> peptide within CHARMM force field. Charges and bonded terms are transferred
> by analogy from available amino acid and lipid parameters. Grompp throwing
> errors for missing dihedral and bond terms of the linkage between ester
> group and peptide backbone. I appreciate any ideas.
>
>
> [image: image.png]
> Thanks
> Raji
>
> --
>
> Message: 2
> Date: Mon, 26 Nov 2018 22:29:07 +0330
> From: rose rahmani 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Distance calculation
> Message-ID:
> 
> Content-Type: text/plain; charset="UTF-8"
>
> Can i use -dist option?
> Would you please help me?
> On Mon, 26 Nov 2018, 00:48 rose rahmani 
> > Hi,
> >
> > My system contains 20 amino acids around nanotube. I want to know the
> > adsorption amount of AA during simulation time; the adsorption occurs
> > when the distance between one of non-hydrogen atoms of AA and the tube
> > surface was less than 0.5 nm. So how can i calculate this property?
> >
> > Would you please help me?
> > Best
> >
>
>
> --
>
> Message: 3
> Date: Mon, 26 Nov 2018 21:51:50 +0100
> From: Mark Abraham 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Interaction energy
> Message-ID:
> 
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> On Mon, Nov 26, 2018 at 7:47 PM Nick Johans  wrote:
>
> > On Mon, 26 Nov 2018, 21:28 Justin Lemkul  >
> > >
> > >
> > > On 11/26/18 10:51 AM, Nick Johans wrote:
> > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  > > >
> > > >>
> > > >> On 11/22/18 11:41 AM, Nick Johans wrote:
> > > >>> Hi
> > > >>>
> > > >>> I am beginner in MD. Maybe it is not a wise question but i want to
> > > >>> calculate the interaction energy between protein and ligand and also
> > > PMF
> > > >> in
> > > >>> different distances. But i don't know what is the didference between
> > > >> PMF, i
> > > >>> mean free energy in particular(by umbrella sampling) and the
> > > interaction
> > > >>> energy (by g_energy tool) in my case?
> > > >> Interaction energy is a pairwise decomposition of short-range
> > nonbonded
> > > >> interaction energy in the system. This energy is usually not
> > physically
> > > >> meaningful, but if the force field has been parametrized in such a way
> > > >> that it is, the interaction energy is a contribution to the enthalpy
> > of
> > > >> the system.
> > > >>
> > > > What forcefields embedded in GROMACS do, yes?
> > >
> > > AFAIK only CHARMM.
> > >
> > Interesting! You mean interaction energy calculated by for example AMBER
> > may not be true? Why?? What makes CHARMM unique??
> >
>
> As Justin said, the difference is in the way it is parametrized.
> Forcefields are generally built to be additive, but it does not follow that
> they are decomposable.
>
> > > If coulomb energy is also existed between pairs, so the interaction
> > > energy
> > > > will be LJ+Coulomb yes?
> > >
> > > Pairs are 1-4 (intramolecular) interactions, so if you define
> > > interaction energy between two nonbonded species, you'll get zeroes for
> > 

[gmx-users] preparing input file for GPU

[Seketoulie Keretsu]

I am running a protein ligand simulation for the first time after
installation of GPU. When i execute mdrun i got this message,
"Multiple energy groups is not implemented for GPUs, falling back to
the CPU. ". I understand i have to remove the energy group in the .mdp
file. But I am not sure how to do that. What are the changes i should
do to make it compatible for GPU execution? Kindly suggest me a
material or link where i can find the information. I have looked at
some gromacs manual but could not really find for the specific
problem. Suggestions on where to look will be appreciated too.

Here is my .mdp file:
title   = Protein-ligand complex MD simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 10; 2 * 10 = 200 ps (0.2 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
nstxout-compressed  = 5000  ; write .xtc trajectory every 10.0 ps
compressed-x-grps   = System
energygrps  = Protein UNK
; Bond parameters
continuation= yes   ; first dynamics run
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
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 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)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_UNK  Water_and_ions; two coupling groups -
more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature,
one for each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal
compressibility of water, bar^-1
; 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
x   x
xxx
x   x
xxx
Thanking you in anticipation.

Seke
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Re: [gmx-users] Charge system simulation problem

[Karpurmanjari Kakati]

Hi Justin,

Because I have self generated the itp file, and that's the only place where
charge in terms of partial charge is added. Is the problem lying there?
Also can't  we denote the partial charges in decimal because  in real some
atoms will have net charges that can be decimal values due to presence or
absence of electronegative atoms adjacent to it?


And are all the other notes and warnings generated are all because of that?


karpurmanjari

On Mon, Nov 26, 2018 at 10:31 AM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:

> Dear All,
>
> My System contains, while doing NVT of the same, I got the following Note
>
>
>
>
>
>
> *NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
> 12.936997  Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for
> discussion on how close it should be to an integer.*
>
>
> This is possibly because of  the partial charges in the molecules in the
> ITP fie.
> My doubt is can't I have a system with non zero and a decimal charge value.
>
>
> Also I got the following warning:
>
>
>
>
>
>
> *WARNING 1 [file sa.top, line 80]:  You are using Ewald electrostatics in
> a system with net charge. This can  lead to severe artifacts, such as ions
> moving into regions with low  dielectric, due to the uniform background
> charge. We suggest to  neutralize your system with counter ions, possibly
> in combination with a  physiological salt concentration.*
>
> Can Someone help me with this?
>
> Also this :
>
>
>
>
>
>
>
> *Velocities were taken from a Maxwell distribution at 300 KRemoving all
> charge groups because cutoff-scheme=VerletAnalysing residue names:There
> are: 1  Other residuesThere are: 10  Water residues*
>
>
> Removing all charge group because the cut off scheme is verlet.
>
> If That happens then will it show the behavior I want to see. Or shall I
> put any other scheme on that ?
>
> Please help
>
>
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[gmx-users] Gromacs 2018.3 Exceeding Memory Issue

[Peiyin Lee]

Hi, all GROMACS users,

   I am trying to run jobs with Gromacs 2018.3 version and constantly got a
memory exceeding error. The system I ran is an all-atom system with 21073
atoms. The largest file that is estimated to be generated is around 5.8 GB.
My jobs got constantly killed after running for only around 15 minutes and
got an error message like this: "slurmstepd: error: Job 12381762 exceeded
memory limit (123122052 > 12288), being killed". I have tried using a
larger memory specification (12GB/core) but it would take too long to wait
and I don't think my job really uses that many memories. I have attached my
.mdp file as below:
"title = NVT Production Run for Trpzip4 in pure H2O

define =; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 5000 ; 0.002 * 5 = 10 ps (100 ns)

dt = 0.002 ; 2 fs

; Output control

nstenergy = 1 ; save energies every 20 ps

nstlog = 1 ; update log file every 20 ps

nstxout-compressed = 1  ; 20ps

compressed-x-precision = 200   ; 0.05

compressed-x-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

; Neighborsearching

ns_type = grid ; search neighboring grid cels

nstlist = 5 ; 10 fs

rlist = 1.2 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; More accurate thermostat

tc-grps = Protein SOL NA; 2 coupling groups - more accurate

tau_t = 0.5 0.5 0.5; time constant, in ps

ref_t = 400 400  400 ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = No  ; Pressure coupling on in NPT

pcoupltype = isotropic ; uniform scaling of x-y box vectors,
independent z

tau_p = 5.0 ; time constant, in ps

ref_p = 1.0 ; reference pressure, x-y, z (in bar)

compressibility = 4.5e-5 ; isothermal compressibility, bar^-1

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation
gen_vel = no ; Velocity generation is off"
and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
-noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo md.cpt
-g md.log". This is my first time posting so please excuse anything that's
unclear. I will try to clarify if needed. Any help is greatly appreciated!

Regards,
Peiyin Lee
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[gmx-users] shameless self-promotion

[Alex]

Hi all,

This isn't a Gromacs question, but a bit of self-promotion with a
not-so-hidden agenda.

1. Here's our paper that I think might be of interest to you beautiful
biophysics folks: https://www.nature.com/articles/s41563-018-0220-4

2. All of this was done with Gromacs. I cannot imagine any other package
capable of providing simulated timescales like this without an actual
supercomputer (we had three GPU-accelerated nodes). We use other MD
packages (which will not be named) and nothing comes close speed-wise. Our
endless love and gratitude go to the developers.

3. GMX developers: We will _NOT_ stop using Gromacs for non-biomolecules!
It can be done and it should be done, and Gromacs works for these systems.
Sometimes with a little bit of system design pain, but it does. Maybe one
day you will find it in your hearts to listen to the solid-state folks and
start extending software capabilities to meet our needs more directly. One
can only hope. ;)

I invite your "wow that's interesting stuff" and other comments here.
Again, thanks!

Alex
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Re: [gmx-users] Interaction energy

[Mark Abraham]

Hi,

On Mon, Nov 26, 2018 at 7:47 PM Nick Johans  wrote:

> On Mon, 26 Nov 2018, 21:28 Justin Lemkul 
> >
> >
> > On 11/26/18 10:51 AM, Nick Johans wrote:
> > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  > >
> > >>
> > >> On 11/22/18 11:41 AM, Nick Johans wrote:
> > >>> Hi
> > >>>
> > >>> I am beginner in MD. Maybe it is not a wise question but i want to
> > >>> calculate the interaction energy between protein and ligand and also
> > PMF
> > >> in
> > >>> different distances. But i don't know what is the didference between
> > >> PMF, i
> > >>> mean free energy in particular(by umbrella sampling) and the
> > interaction
> > >>> energy (by g_energy tool) in my case?
> > >> Interaction energy is a pairwise decomposition of short-range
> nonbonded
> > >> interaction energy in the system. This energy is usually not
> physically
> > >> meaningful, but if the force field has been parametrized in such a way
> > >> that it is, the interaction energy is a contribution to the enthalpy
> of
> > >> the system.
> > >>
> > > What forcefields embedded in GROMACS do, yes?
> >
> > AFAIK only CHARMM.
> >
> Interesting! You mean interaction energy calculated by for example AMBER
> may not be true? Why?? What makes CHARMM unique??
>

As Justin said, the difference is in the way it is parametrized.
Forcefields are generally built to be additive, but it does not follow that
they are decomposable.

> > If coulomb energy is also existed between pairs, so the interaction
> > energy
> > > will be LJ+Coulomb yes?
> >
> > Pairs are 1-4 (intramolecular) interactions, so if you define
> > interaction energy between two nonbonded species, you'll get zeroes for
> > all the pair energies, by definition.
> >
> It's exactly the SR(short range) selection in g_energy, yes?


You seem to be using a looser definition of pairs than is usual in
discussion of GROMACS topologies.


> all long range
> are zero.


If there's a long-range model, then such interactions are not uniformly of
zero magnitude...


> But coulomb and LJ are non-zero. So, in this case the interaction
> energy would be
> Short range LJ+ Short range Coulomb , true?
>

As far as I'm concerned, you can invent whatever quantity you want, but the
burden is on you to demonstrate that there's a reason to connect it to
something physical.

Mark


> >
> > > So what about PMF. It seems like an interaction energy too, but more
> > > accurate one???
> >
> > That's not what a PMF is. A PMF is the change in free energy of a system
> > as a function of progress along a reaction coordinate.
> >
> > -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
> >
> > * 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.
> >
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Re: [gmx-users] Distance calculation

[rose rahmani]

Can i use -dist option?
Would you please help me?
On Mon, 26 Nov 2018, 00:48 rose rahmani  Hi,
>
> My system contains 20 amino acids around nanotube. I want to know the
> adsorption amount of AA during simulation time; the adsorption occurs
> when the distance between one of non-hydrogen atoms of AA and the tube
> surface was less than 0.5 nm. So how can i calculate this property?
>
> Would you please help me?
> Best
>
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[gmx-users] Parameterizing N-terminal capping

[Raji]

Hi

I am trying to parameterize the N-terminal ‘carboxybenzyl’ capping for
peptide within CHARMM force field. Charges and bonded terms are transferred
by analogy from available amino acid and lipid parameters. Grompp throwing
errors for missing dihedral and bond terms of the linkage between ester
group and peptide backbone. I appreciate any ideas.


[image: image.png]
Thanks
Raji
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Re: [gmx-users] Interaction energy

[Nick Johans]

On Mon, 26 Nov 2018, 21:28 Justin Lemkul 
>
> On 11/26/18 10:51 AM, Nick Johans wrote:
> > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  >
> >>
> >> On 11/22/18 11:41 AM, Nick Johans wrote:
> >>> Hi
> >>>
> >>> I am beginner in MD. Maybe it is not a wise question but i want to
> >>> calculate the interaction energy between protein and ligand and also
> PMF
> >> in
> >>> different distances. But i don't know what is the didference between
> >> PMF, i
> >>> mean free energy in particular(by umbrella sampling) and the
> interaction
> >>> energy (by g_energy tool) in my case?
> >> Interaction energy is a pairwise decomposition of short-range nonbonded
> >> interaction energy in the system. This energy is usually not physically
> >> meaningful, but if the force field has been parametrized in such a way
> >> that it is, the interaction energy is a contribution to the enthalpy of
> >> the system.
> >>
> > What forcefields embedded in GROMACS do, yes?
>
> AFAIK only CHARMM.
>
Interesting! You mean interaction energy calculated by for example AMBER
may not be true? Why?? What makes CHARMM unique??

>
> > If coulomb energy is also existed between pairs, so the interaction
> energy
> > will be LJ+Coulomb yes?
>
> Pairs are 1-4 (intramolecular) interactions, so if you define
> interaction energy between two nonbonded species, you'll get zeroes for
> all the pair energies, by definition.
>
It's exactly the SR(short range) selection in g_energy, yes? all long range
are zero. But coulomb and LJ are non-zero. So, in this case the interaction
energy would be
Short range LJ+ Short range Coulomb , true?

>
> > So what about PMF. It seems like an interaction energy too, but more
> > accurate one???
>
> That's not what a PMF is. A PMF is the change in free energy of a system
> as a function of progress along a reaction coordinate.
>
> -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
>
> * For (un)subscribe requests visit
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Re: [gmx-users] Interaction energy

[Justin Lemkul]

On 11/26/18 1:35 PM, rose rahmani wrote:

On Mon, 26 Nov 2018, 21:28 Justin Lemkul 

On 11/26/18 10:51 AM, Nick Johans wrote:

On Mon, 26 Nov 2018, 18:22 Justin Lemkul 
On 11/22/18 11:41 AM, Nick Johans wrote:

Hi

I am beginner in MD. Maybe it is not a wise question but i want to
calculate the interaction energy between protein and ligand and also

PMF

in

different distances. But i don't know what is the didference between

PMF, i

mean free energy in particular(by umbrella sampling) and the

interaction

energy (by g_energy tool) in my case?

Interaction energy is a pairwise decomposition of short-range nonbonded
interaction energy in the system. This energy is usually not physically
meaningful, but if the force field has been parametrized in such a way
that it is, the interaction energy is a contribution to the enthalpy of
the system.


What forcefields embedded in GROMACS do, yes?

AFAIK only CHARMM.


If coulomb energy is also existed between pairs, so the interaction

energy

will be LJ+Coulomb yes?

Pairs are 1-4 (intramolecular) interactions, so if you define
interaction energy between two nonbonded species, you'll get zeroes for
all the pair energies, by definition.


So what about PMF. It seems like an interaction energy too, but more
accurate one???

That's not what a PMF is. A PMF is the change in free energy of a system
as a function of progress along a reaction coordinate.


If interaction energy between protein1 and special ligand is more than
between protein2 and that ligand, it is tru its free energy would also be
more than it?


No, because you know nothing about desolvation penalty and loss of 
entropy upon binding.


-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] Interaction energy

[rose rahmani]

On Mon, 26 Nov 2018, 21:28 Justin Lemkul 
>
> On 11/26/18 10:51 AM, Nick Johans wrote:
> > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  >
> >>
> >> On 11/22/18 11:41 AM, Nick Johans wrote:
> >>> Hi
> >>>
> >>> I am beginner in MD. Maybe it is not a wise question but i want to
> >>> calculate the interaction energy between protein and ligand and also
> PMF
> >> in
> >>> different distances. But i don't know what is the didference between
> >> PMF, i
> >>> mean free energy in particular(by umbrella sampling) and the
> interaction
> >>> energy (by g_energy tool) in my case?
> >> Interaction energy is a pairwise decomposition of short-range nonbonded
> >> interaction energy in the system. This energy is usually not physically
> >> meaningful, but if the force field has been parametrized in such a way
> >> that it is, the interaction energy is a contribution to the enthalpy of
> >> the system.
> >>
> > What forcefields embedded in GROMACS do, yes?
>
> AFAIK only CHARMM.
>
> > If coulomb energy is also existed between pairs, so the interaction
> energy
> > will be LJ+Coulomb yes?
>
> Pairs are 1-4 (intramolecular) interactions, so if you define
> interaction energy between two nonbonded species, you'll get zeroes for
> all the pair energies, by definition.
>
> > So what about PMF. It seems like an interaction energy too, but more
> > accurate one???
>
> That's not what a PMF is. A PMF is the change in free energy of a system
> as a function of progress along a reaction coordinate.
>
If interaction energy between protein1 and special ligand is more than
between protein2 and that ligand, it is tru its free energy would also be
more than it?

>
> -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
>
> * 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.
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[gmx-users] -t state.cpt

[hosein geraili]

Hi all,
What would happen if someone would not use -t previous_state.cpt in the 
production run?? Isn't that the case that gromacs can read the velocity from 
the last frame .gro file of the previous simulation?
Best
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Re: [gmx-users] Interaction energy

[Justin Lemkul]

On 11/26/18 10:51 AM, Nick Johans wrote:

On Mon, 26 Nov 2018, 18:22 Justin Lemkul 

On 11/22/18 11:41 AM, Nick Johans wrote:

Hi

I am beginner in MD. Maybe it is not a wise question but i want to
calculate the interaction energy between protein and ligand and also PMF

in

different distances. But i don't know what is the didference between

PMF, i

mean free energy in particular(by umbrella sampling) and the interaction
energy (by g_energy tool) in my case?

Interaction energy is a pairwise decomposition of short-range nonbonded
interaction energy in the system. This energy is usually not physically
meaningful, but if the force field has been parametrized in such a way
that it is, the interaction energy is a contribution to the enthalpy of
the system.


What forcefields embedded in GROMACS do, yes?


AFAIK only CHARMM.


If coulomb energy is also existed between pairs, so the interaction energy
will be LJ+Coulomb yes?


Pairs are 1-4 (intramolecular) interactions, so if you define 
interaction energy between two nonbonded species, you'll get zeroes for 
all the pair energies, by definition.



So what about PMF. It seems like an interaction energy too, but more
accurate one???


That's not what a PMF is. A PMF is the change in free energy of a system 
as a function of progress along a reaction coordinate.


-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] Fwd: Mismatch between gromacs and python-networkx versions

[Justin Lemkul]

On 11/26/18 12:54 PM, Francesco Pietra wrote:

Hurrying - as with my post above - is seldom a good procedure.
The next step, converting ligand_ini.pdb to ligand.gro did not work well,
i.e., for GDP the .gro file reads
S  C  A  M  O  R  G
40
 0/scrPB1   0.100   0.000   0.100
 0/scr   O1B2   0.100   0.000   0.100
 0/scr   O2B3   0.100   0.000   0.100
 0/scr   O3B4   0.100   0.000   0.100
 0/scr   O3A5   0.100   0.000   0.100
 0/scrPA6   0.100   0.000   0.100

which came anyway unespected as the ligand_ini.pdb looks like to be correct

ATOM  1 PB   /scratch/phpK1JFey_GDP_H.pdb1 320.960 448.853
308.012  1.00  0.00
ATOM  2 O1B  /scratch/phpK1JFey_GDP_H.pdb1 320.256 449.824
307.091  1.00  0.00
ATOM  3 O2B  /scratch/phpK1JFey_GDP_H.pdb1 320.922 447.397
307.609  1.00  0.00
ATOM  4 O3B  /scratch/phpK1JFey_GDP_H.pdb1 320.622 449.126
309.460  1.00  0.00
ATOM  5 O3A  /scratch/phpK1JFey_GDP_H.pdb1 322.508 449.269
307.860  1.00  0.00
ATOM  6 PA   /scratch/phpK1JFey_GDP_H.pdb1 323.692 448.599
308.726  1.00  0.00
ATOM  7 O1A  /scratch/phpK1JFey_GDP_H.pdb1 324.384 447.624
307.801  1.00  0.00 came unexpected, as the ligand_ini.pdb looks like to be
correct


You need a sensible name in your @TRIPOS definition, with no 
more than 4 characters. Your file has the name of a full path to a file 
in it.


-Justin


fp

-- Forwarded message -
From: Francesco Pietra 
Date: Mon, Nov 26, 2018 at 6:25 PM
Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
versions
To: 


This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul  wrote:



On 11/25/18 9:10 AM, Francesco Pietra wrote:

This is my first post to gromacs, to which I came in the hope that FEP
simulations are more efficient than with other engines.

I updated debian amd64 from stretch to buster in order to have the said
preferred gromacs 2018 (2016 on stretch). Now, to set up the system
(protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
is required. Am I wrong, or there is really such a mismatch?. If so, how

to

turn around? I have only one version of linux.

GROMACS has no NetworkX requirement. If you're talking about the
cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
for it to work. But that's not a GROMACS issue.

-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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--
==

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] Fwd: Mismatch between gromacs and python-networkx versions

[Francesco Pietra]

Hurrying - as with my post above - is seldom a good procedure.
The next step, converting ligand_ini.pdb to ligand.gro did not work well,
i.e., for GDP the .gro file reads
S  C  A  M  O  R  G
   40
0/scrPB1   0.100   0.000   0.100
0/scr   O1B2   0.100   0.000   0.100
0/scr   O2B3   0.100   0.000   0.100
0/scr   O3B4   0.100   0.000   0.100
0/scr   O3A5   0.100   0.000   0.100
0/scrPA6   0.100   0.000   0.100

which came anyway unespected as the ligand_ini.pdb looks like to be correct

ATOM  1 PB   /scratch/phpK1JFey_GDP_H.pdb1 320.960 448.853
308.012  1.00  0.00
ATOM  2 O1B  /scratch/phpK1JFey_GDP_H.pdb1 320.256 449.824
307.091  1.00  0.00
ATOM  3 O2B  /scratch/phpK1JFey_GDP_H.pdb1 320.922 447.397
307.609  1.00  0.00
ATOM  4 O3B  /scratch/phpK1JFey_GDP_H.pdb1 320.622 449.126
309.460  1.00  0.00
ATOM  5 O3A  /scratch/phpK1JFey_GDP_H.pdb1 322.508 449.269
307.860  1.00  0.00
ATOM  6 PA   /scratch/phpK1JFey_GDP_H.pdb1 323.692 448.599
308.726  1.00  0.00
ATOM  7 O1A  /scratch/phpK1JFey_GDP_H.pdb1 324.384 447.624
307.801  1.00  0.00 came unexpected, as the ligand_ini.pdb looks like to be
correct

fp

-- Forwarded message -
From: Francesco Pietra 
Date: Mon, Nov 26, 2018 at 6:25 PM
Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
versions
To: 


This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul  wrote:

>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -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
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Re: [gmx-users] pH Replica Exchange

[Reza Esmaeeli]

As I guessed. Thanks.

On Monday, November 26, 2018, Justin Lemkul  wrote:

>
>
> On 11/26/18 4:50 AM, Reza Esmaeeli wrote:
>
>> I’m considering Replica Exchange MD for different pH values with GROMACS.
>> Any ideas where to start?
>>
>> (In the literature, this is usually done using Amber or CHARMM packages)
>>
>
> Start by using AMBER or CHARMM :)
>
> AFAIK, there is no support for anything like this in GROMACS.
>
> -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] Mismatch between gromacs and python-networkx versions

[Francesco Pietra]

This is to let you know, that the fixed .mol2 (got by first removing #
comments, as you indicated), the script cgenff_charmm2gmx.py works well
with the NetworkX 2x and charmm36-nov2018.ff. I still have to run gromacs
with them, but the content of the files looks like to be what was expected.
fp

thanks again

On Mon, Nov 26, 2018 at 3:57 PM Justin Lemkul  wrote:

>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -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] rdf coordination number over time (ns)

[Arun Srikanth]

Hi if you have rdf it is easy to calculate the coordination number by
numerical integration

https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions

Arun

On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa  wrote:

> Dear users,
> I need to calculate rdf coordination number over time. I have a pdb
> trajecory of 200 ns, from which I want to evaluate  g(r) and CN of Na-Cl,
> Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number
> in function of time! Can you help me?
>
> Maria Luisa
>
>
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perro...@itm.cnr.it
>
>
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[gmx-users] rdf coordination number over time (ns)

[Maria Luisa]

Dear users,
I need to calculate rdf coordination number over time. I have a pdb
trajecory of 200 ns, from which I want to evaluate  g(r) and CN of Na-Cl,
Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number
in function of time! Can you help me?

Maria Luisa


Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
Italy
email: ml.perro...@itm.cnr.it


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[gmx-users] make_ndx and assigning velocities

[Ali Khodayari]

Dear Gmx users,

 

I have two questions. 

 

I am wondering how I can assign residues from different chains to one single
index group? Say, residues 50 to 70 of first chain and residues 120 to 140
of the second chain.

 

Secondly, how can I assign velocities to certain groups? For instance, to
restrain the positions of one group (V = 0) and to assign a certain velocity
(V ~= 0) to another group?

 

Thank you for your help.

 

Kind regards,

Ali 

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Re: [gmx-users] Interaction energy

[Nick Johans]

On Mon, 26 Nov 2018, 18:22 Justin Lemkul 
>
> On 11/22/18 11:41 AM, Nick Johans wrote:
> > Hi
> >
> > I am beginner in MD. Maybe it is not a wise question but i want to
> > calculate the interaction energy between protein and ligand and also PMF
> in
> > different distances. But i don't know what is the didference between
> PMF, i
> > mean free energy in particular(by umbrella sampling) and the interaction
> > energy (by g_energy tool) in my case?
>
> Interaction energy is a pairwise decomposition of short-range nonbonded
> interaction energy in the system. This energy is usually not physically
> meaningful, but if the force field has been parametrized in such a way
> that it is, the interaction energy is a contribution to the enthalpy of
> the system.
>
What forcefields embedded in GROMACS do, yes?
If coulomb energy is also existed between pairs, so the interaction energy
will be LJ+Coulomb yes?

So what about PMF. It seems like an interaction energy too, but more
accurate one???

>
> -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] gromacs.org_gmx-users Digest, Vol 175, Issue 91

[Elias Santos]

Dear Justin,

Thanks for answer.

On Mon, Nov 26, 2018 at 1:01 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: free binding energy calculation (Justin Lemkul)
>2. Re: sort_mol2_bonds.pl issues (Justin Lemkul)
>3. Re: Mismatch between gromacs and python-networkx  versions
>   (Justin Lemkul)
>4. Re: Charge system simulation problem (Justin Lemkul)
>5. Re: pH Replica Exchange (Justin Lemkul)
>6. Re: ionize flag (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Mon, 26 Nov 2018 09:55:30 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] free binding energy calculation
> Message-ID: <327a86c6-3e7d-1bc3-931b-addacd3b7...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/23/18 4:07 PM, marzieh dehghan wrote:
> > Thanks a lot for your kind answer, I used the same link to calculate free
> > binding energy and confront the mentioned error.
>
> Please make sure to use a correct subject, and don't reply to the entire
> digest. If you're actively asking/answering questions, I suggest
> subscribing in individual message mode, not digest.
>
> To the original question, if you follow the tutorial and use the files
> at the correct link (mdtutorials.com/gmx), you cannot possibly get the
> error you mentioned before. The old tutorials on the
> bevanlab.biochem.vt.edu site should not be used any more. They are
> outdated and should go offline soon, anyway. The input files on
> mdtutorials.com/gmx are updated and correct for version 2018. You will
> not get the same error.
>
> -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
>
> ==
>
>
>
> --
>
> Message: 2
> Date: Mon, 26 Nov 2018 09:56:20 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] sort_mol2_bonds.pl issues
> Message-ID: <6da7eec2-e98f-eb26-0db8-de912e285...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/26/18 2:46 AM, Francesco Pietra wrote:
> > Hi
> > sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandb
> tutorial)
> > does not work for me. The .mol2 file is simply stripped out of the whole
> > list of bonds, while the atom list remain not ordered (for example oxygen
> > before carbon, or C13 before C1). This occurs with also monotone atom
> > numbering. But I also have cases with also hyphenated due to the presence
> > of side chains. An excerpt from the universal GDP
> > 1  PB   320.9600  448.8530  308.0120 P.3   501  GDP 0.5373
> >2  O1B  320.2560  449.8240  307.0910 O.3   501  GDP
> -0.1143
> >3  O2B  320.9220  447.3970  307.6090 O.3   501  GDP
> -0.1143
> >4  O3B  320.6220  449.1260  309.4600 O.2   501  GDP
> -0.2221
> >5  O3A  322.5080  449.2690  307.8600 O.3   501  GDP
> -0.2261
> >6  PA   323.6920  448.5990  308.7260 P.3   501  GDP
>  0.2224
> >7  O1A  324.3840  447.6240  307.8010 O.3   501  GDP
> -0.4370
> >8  O2A  323.1200  447.9850  309.9830 O.2   501  GDP
> -0.5170
> >9  O5'  324.6580  449.8470  309.1210 O.3   501  GDP
> -0.3245
> >   10  C5'  326.0610  449.8930  308.8080 C.3   501  GDP
>  0.0836
> >   11  C4'  326.9510  449.9750  310.0480 C.3   501  GDP
>  0.1133
> >   12  O4'  326.8250  448.7650  310.8190 O.3   501  GDP
> -0.3456
> >   13  C3'  328.4210  450.0360  309.6490 C.3   501  GDP
>  0.1135
> >
> > Did not find anything about on Internet.
>
> Please send me your .mol2 file off-list. The script doesn't do anything
> to the atoms, only the bonds, so I can't tell what's going on. As this
> is not a GROMACS problem, please just contact me directly about the issue.
>
> -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.

Re: [gmx-users] ionize flag

[Justin Lemkul]

On 11/26/18 8:34 AM, Elias Santos wrote:

Hi everyone!!
I'm working with a system in gas-phase, where in the first simulation I use
the command mdrun -deffnm mdall -v. In the second one, it is bombarded with
X-ray using the -[yes]ionize flag gromacs 4.5.6. However, comparing the two
simulations I have observed that the values for energies are the same. So,
there is something wrong.
Could you help me!!


That featured was removed a long time ago because it was unmaintained 
and no one was sure if it worked. Likely it simply doesn't work.


-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] pH Replica Exchange

[Justin Lemkul]

On 11/26/18 4:50 AM, Reza Esmaeeli wrote:

I’m considering Replica Exchange MD for different pH values with GROMACS.
Any ideas where to start?

(In the literature, this is usually done using Amber or CHARMM packages)


Start by using AMBER or CHARMM :)

AFAIK, there is no support for anything like this in GROMACS.

-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] Charge system simulation problem

[Justin Lemkul]

On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote:

Dear All,

My System contains, while doing NVT of the same, I got the following Note






*NOTE 1 [file sa.top, line 80]:  System has non-zero total charge:
12.936997  Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for
discussion on how close it should be to an integer.*


This is possibly because of  the partial charges in the molecules in the
ITP fie.


Something isn't parametrized correctly because you need to have an 
integer charge. Your total charge is not physical.


-Justin


My doubt is can't I have a system with non zero and a decimal charge value.


Also I got the following warning:






*WARNING 1 [file sa.top, line 80]:  You are using Ewald electrostatics in a
system with net charge. This can  lead to severe artifacts, such as ions
moving into regions with low  dielectric, due to the uniform background
charge. We suggest to  neutralize your system with counter ions, possibly
in combination with a  physiological salt concentration.*

Can Someone help me with this?

Also this :







*Velocities were taken from a Maxwell distribution at 300 KRemoving all
charge groups because cutoff-scheme=VerletAnalysing residue names:There
are: 1  Other residuesThere are: 10  Water residues*


Removing all charge group because the cut off scheme is verlet.

If That happens then will it show the behavior I want to see. Or shall I
put any other scheme on that ?

Please help


--
==

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] Mismatch between gromacs and python-networkx versions

[Justin Lemkul]

On 11/25/18 9:10 AM, Francesco Pietra wrote:

This is my first post to gromacs, to which I came in the hope that FEP
simulations are more efficient than with other engines.

I updated debian amd64 from stretch to buster in order to have the said
preferred gromacs 2018 (2016 on stretch). Now, to set up the system
(protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
is required. Am I wrong, or there is really such a mismatch?. If so, how to
turn around? I have only one version of linux.


GROMACS has no NetworkX requirement. If you're talking about the 
cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11 
for it to work. But that's not a GROMACS issue.


-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] sort_mol2_bonds.pl issues

[Justin Lemkul]

On 11/26/18 2:46 AM, Francesco Pietra wrote:

Hi
sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandb tutorial)
does not work for me. The .mol2 file is simply stripped out of the whole
list of bonds, while the atom list remain not ordered (for example oxygen
before carbon, or C13 before C1). This occurs with also monotone atom
numbering. But I also have cases with also hyphenated due to the presence
of side chains. An excerpt from the universal GDP
1  PB   320.9600  448.8530  308.0120 P.3   501  GDP 0.5373
   2  O1B  320.2560  449.8240  307.0910 O.3   501  GDP-0.1143
   3  O2B  320.9220  447.3970  307.6090 O.3   501  GDP-0.1143
   4  O3B  320.6220  449.1260  309.4600 O.2   501  GDP-0.2221
   5  O3A  322.5080  449.2690  307.8600 O.3   501  GDP-0.2261
   6  PA   323.6920  448.5990  308.7260 P.3   501  GDP 0.2224
   7  O1A  324.3840  447.6240  307.8010 O.3   501  GDP-0.4370
   8  O2A  323.1200  447.9850  309.9830 O.2   501  GDP-0.5170
   9  O5'  324.6580  449.8470  309.1210 O.3   501  GDP-0.3245
  10  C5'  326.0610  449.8930  308.8080 C.3   501  GDP 0.0836
  11  C4'  326.9510  449.9750  310.0480 C.3   501  GDP 0.1133
  12  O4'  326.8250  448.7650  310.8190 O.3   501  GDP-0.3456
  13  C3'  328.4210  450.0360  309.6490 C.3   501  GDP 0.1135

Did not find anything about on Internet.


Please send me your .mol2 file off-list. The script doesn't do anything 
to the atoms, only the bonds, so I can't tell what's going on. As this 
is not a GROMACS problem, please just contact me directly about the issue.


-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] free binding energy calculation

[Justin Lemkul]

On 11/23/18 4:07 PM, marzieh dehghan wrote:

Thanks a lot for your kind answer, I used the same link to calculate free
binding energy and confront the mentioned error.


Please make sure to use a correct subject, and don't reply to the entire 
digest. If you're actively asking/answering questions, I suggest 
subscribing in individual message mode, not digest.


To the original question, if you follow the tutorial and use the files 
at the correct link (mdtutorials.com/gmx), you cannot possibly get the 
error you mentioned before. The old tutorials on the 
bevanlab.biochem.vt.edu site should not be used any more. They are 
outdated and should go offline soon, anyway. The input files on 
mdtutorials.com/gmx are updated and correct for version 2018. You will 
not get the same error.


-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] (no subject)

[Justin Lemkul]

On 11/23/18 12:58 AM, maya nair wrote:

I am trying to do the molecular dynamics of  DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp  ions.mdp and em.mdp, it gives error saying the following

Command line:
   gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
   Too few gb parameters for type 1


Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.


The .atp file is only read by pdb2gmx, so it's not relevant. Apparently 
you have an atom type "1" (number one) in your topology, which is very 
strange. It doesn't have parameters defined in gb.itp, so you get a 
failure. Make sure your input is sound and your topology/force field 
files are free of typos.



Help me in this regard. I am attaching my files.


This mailing list does not accept attachments. If you need to share 
files, use a file-sharing service and provide the URL.


-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] Interaction energy

[Justin Lemkul]

On 11/22/18 11:41 AM, Nick Johans wrote:

Hi

I am beginner in MD. Maybe it is not a wise question but i want to
calculate the interaction energy between protein and ligand and also PMF in
different distances. But i don't know what is the didference between PMF, i
mean free energy in particular(by umbrella sampling) and the interaction
energy (by g_energy tool) in my case?


Interaction energy is a pairwise decomposition of short-range nonbonded 
interaction energy in the system. This energy is usually not physically 
meaningful, but if the force field has been parametrized in such a way 
that it is, the interaction energy is a contribution to the enthalpy of 
the system.


-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] Implementation of drude simulation

[Justin Lemkul]

On 11/22/18 9:37 AM, Gonzalo Quezada wrote:

Greetings gromacs users,

I'm trying to run a simulation of polarizable water and ions with the
drude-2013 forcefield. I use the simulation parameters from the supporting
information from "Implementation of Extended Lagrangian Dynamics in GROMACS
for Polarizable Simulations Using the Classical Drude Oscillator Model".


Please note that this implementation remains developmental and therefore 
is not officially supported yet. Most features work but I still haven't 
completed the domain decomposition code re-write.



In pure water (SWM4-NDP) I have no issues, but when I incorporate ions like
Na and Cl most of the simulation crash. Also, the message of HARDWALL
appear at every step for the ions. I studied the simulations to find when
and how the crash is produce but without success because the reasons are
not sistematic.


If you're trying to run with DD, then these failures are spurious. If 
you're using OpenMP to parallelize, then you probably haven't adequately 
minimized/equilibrated the system. It is extremely easy to break a 
polarizable simulation, particularly in the early stages.



I'm still learing so I think maybe the simulations parameters that I put
are not the best suitable for ions.


You haven't given any useful diagnostic information, such as what steps 
you've taken or what input settings you're using, so there's not much to 
go on to help you.


-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] Printing only center of mass of during simulation

[Justin Lemkul]

On 11/22/18 6:39 AM, Sudarshan Behera wrote:

Hello Gromacs Users,
  I wanted to know if there is any way to print only the *centre of mass* of
a user defined group(instead of all the x,y,z coordinates) during
simulation run (mdrun).


There is no such feature. You can extract this information after the 
fact from the trajectory using gmx traj -ox -com.


-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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[gmx-users] Gmx distance

[rose rahmani]

Hi,

I use gmx distance -dist 1.5 -f -s -n -o dist.xvg and select ZnS and
Protein-H groups.
Why i couldn't get any output file? Ot is processing during analuzing but
it doesn't have any dist.xvg and output file. When i use option -lt the
lifetime.xvg is empty. But i know there are distances closer than 1.5 nm
between ZnS and all non-hydrogwm atoms. How could it be possible?
I will be appreciatex if you help me.
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[gmx-users] ionize flag

[Elias Santos]

Hi everyone!!
I'm working with a system in gas-phase, where in the first simulation I use
the command mdrun -deffnm mdall -v. In the second one, it is bombarded with
X-ray using the -[yes]ionize flag gromacs 4.5.6. However, comparing the two
simulations I have observed that the values for energies are the same. So,
there is something wrong.
Could you help me!!


Elias
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[gmx-users] pH Replica Exchange

[Reza Esmaeeli]

I’m considering Replica Exchange MD for different pH values with GROMACS.
Any ideas where to start?

(In the literature, this is usually done using Amber or CHARMM packages)

Thanks,
Reza
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[gmx-users] HOW TO EXTEND A .XTC FILE ??

[sky sky]

Hello. I am running the MD simulations for 100ns using GROMACS software. Now, I 
have a .xtc file and  I would like to extend my simulation but not from final 
step. Could anyone suggest me how should I extend this .xtc file from specific 
frame for another 100ns and when it ended I just have one .xtc file? it has a 
command? How should I proceed? Thank you in advance for your suggestions. 
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