Re: [gmx-users] No performance increase with single vs multiple nodes

[Mark Abraham]

Hi,

On Sun, Oct 8, 2017 at 2:40 AM Matthew W Hanley  wrote:

> I am running gromacs 2016.3 on CentOS 7.3 with the following command using
> a PBS scheduler:
>
>
> #PBS -N TEST
>
> #PBS -l nodes=1:ppn=32
>
> export OMP_NUM_THREADS=1
>
> mpirun -N 32  mdrun_mpi -deffnm TEST -dlb yes -pin on -nsteps 5 -cpi
> TEST
>
>
> However, I am seeing no performance increase when using more nodes:
>
> On 32 MPI ranks
>Core t (s)   Wall t (s)(%)
>Time:28307.873  884.621 3200.0
>  (ns/day)(hour/ns)
> Performance:  195.3400.123
>
> On 64 MPI ranks
>Core t (s)   Wall t (s)(%)
>Time:25502.709  398.480 6400.0
>  (ns/day)(hour/ns)
> Performance:  216.8280.111
>
> On 96 MPI ranks
>Core t (s)   Wall t (s)(%)
>Time:51977.705  541.434 9600.0
>  (ns/day)(hour/ns)
> Performance:  159.5790.150
>
> On 128 MPI ranks
>Core t (s)   Wall t (s)(%)
>Time:   111576.333  871.69012800.0
>  (ns/day)(hour/ns)
> Performance:  198.2380.121
>
> ?
>

There's several dozen lines of performance analysis at the end of the log
file, which you need to inspect and compare if you want to start to
understand what is going on :-)


> Doing an strace of the mdrun process shows mostly this:
>

strace is not a profiling tool. That's a bit like trying to understand the
performance of 100m sprinters by counting how often they call their
relatives on the phone. ;-) GROMACS does lots of arithmetic, not lots of
calls to system functions.

Mark
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Re: [gmx-users] Equilibration using position restraints in NPT

[Mark Abraham]

On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi  wrote:

> Thank you Mark.
>
> The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
> solvate using spc216.gro.
>

Please visualize that result. Such a command would put solvent all around
your nanotube, so it could not have an infinite topology and be stable.

How can I calculate box size after NVT so that I get density of 1 or 0.99
> when using pressure coupling?
>

Your z dimension is chosen by the size of the nanotube. Your x and y might
be chosen by whatever the above procedure suggests, but you can't actually
use the box that it produced.

Mark
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Re: [gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

[Alex]

I just replied to Neha's post. You are having issues that have nothing 
to do with Gromacs, i.e. Gromacs is simply responding to incorrect 
system setup. Please generate a proper periodic topology and use a 
PBC-compatible box.


Alex


On 10/8/2017 3:47 PM, Ming Tang wrote:

Dear list,

I have gone through carbon nanotube guide on GROMACS website.
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
I have a nanotube aligned to z-direction. I am trying to simulate infinite 
nanotube using periodic conditions. There are issues while simulating this 
system when pressure coupling is used.

GROMACS or other mailing list doesn't provide mdp files for simulation of 
carbon nanotube using NPT ensemble. It appears that we cannot freeze groups to 
constrain nanotube in NPT ensemble. We might have to use position restraints 
for nanotube (most papers report this). I have imposed position restraints on 
nanotube and in doing so, the z coordinates fluctuates by 0.5-1 nm in Z 
direction. This is not an issue with NVT simulation.

How do I equilibrate nanotube system using pressure coupling for 
nonotube/graphene etc with infinite long surface? Should we use semi-isotropic 
scheme (not apply pressure along the axis of nanotube) for pressure coupling or 
it should be isotropic?

P.S.: the force field is opls based on gromacs tutorial and GROMACS version is 
5.1.4. Temperature coupling -V-rescale

Thanks,
Ming on behalf of Neha


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[gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

[Ming Tang]

Dear list,

I have gone through carbon nanotube guide on GROMACS website.
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
I have a nanotube aligned to z-direction. I am trying to simulate infinite 
nanotube using periodic conditions. There are issues while simulating this 
system when pressure coupling is used.

GROMACS or other mailing list doesn't provide mdp files for simulation of 
carbon nanotube using NPT ensemble. It appears that we cannot freeze groups to 
constrain nanotube in NPT ensemble. We might have to use position restraints 
for nanotube (most papers report this). I have imposed position restraints on 
nanotube and in doing so, the z coordinates fluctuates by 0.5-1 nm in Z 
direction. This is not an issue with NVT simulation.

How do I equilibrate nanotube system using pressure coupling for 
nonotube/graphene etc with infinite long surface? Should we use semi-isotropic 
scheme (not apply pressure along the axis of nanotube) for pressure coupling or 
it should be isotropic?

P.S.: the force field is opls based on gromacs tutorial and GROMACS version is 
5.1.4. Temperature coupling -V-rescale

Thanks,
Ming on behalf of Neha
-- 
Gromacs Users mailing list

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Re: [gmx-users] Equilibration using position restraints in NPT

[Alex]

In addition, the CNT edges have to be periodically commensurate.


On 10/8/2017 3:36 PM, Alex wrote:
PBC for crystals are not set this way, this is why the simulator is 
turning the CNT into a pogo stick.


Prior to any simulations, please calculate the correct PBC-compatible 
axial length using crystallographic considerations and CNT chirality, 
-box properly, generate topology with PBC, then proceed with EM, etc.


Alex


On 10/8/2017 3:29 PM, Neha Gandhi wrote:

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  
2 and

solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 
0.99

when using pressure coupling?






Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:

Content-Type: text/plain; charset="UTF-8"

This is a very common post on previous mailing list however, I am 
still not

able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to 
simulate
infinite nanotube using periodic conditions. It is common to use 
position
restraints for nanotube (most papers report this). I have imposed 
position
restraints on nanotube and in doing so, the coordinates fluctuates 
by 0.5-1

nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title    = OPLS Lysozyme NPT equilibration
define    = -DPOSRES_CNT    ; position restrain the protein
; Run parameters
integrator    = md    ; leap-frog integrator
nsteps    = 50    ; 2
dt    = 0.001    ; 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
;energygrps   = Protein  CNT Water NA
; 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
cutoff-scheme   = Verlet
ns_type    = grid    ; search neighboring grid cells
nstlist    = 10    ; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb    = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw    = 1.0    ; 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    = Berendsen    ; modified Berendsen
thermostat
tc-grps    = CNT Water    ; two coupling groups - more accurate
tau_t    = 0.2  0.2    ; time constant, in ps
ref_t    = 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl    = Berendsen    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling 
of box

vectors
tau_p    = 5.0    ; 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
periodic_molecules = yes
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel    = no    ; Velocity generation is off

--
Regards,
Dr. Neha S. Gandhi,


--

Message: 2
Date: Sun, 8 Oct 2017 22:34:21 +0530
From: Dilip H N 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding charges for atoms in a molecule
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using 
charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f 
abc.pdb -o

abc.gro command.
1] In the topology file, the charges for each atom are assigned. 
from where

are these charges assigned..?? is it from the .rtp file, itp file..

Re: [gmx-users] Equilibration using position restraints in NPT

[Alex]

PBC for crystals are not set this way, this is why the simulator is 
turning the CNT into a pogo stick.


Prior to any simulations, please calculate the correct PBC-compatible 
axial length using crystallographic considerations and CNT chirality, 
-box properly, generate topology with PBC, then proceed with EM, etc.


Alex


On 10/8/2017 3:29 PM, Neha Gandhi wrote:

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?






Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:
 
Content-Type: text/plain; charset="UTF-8"

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title= OPLS Lysozyme NPT equilibration
define= -DPOSRES_CNT; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2
dt= 0.001; 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
;energygrps   = Protein  CNT Water NA
; 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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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= Berendsen; modified Berendsen
thermostat
tc-grps= CNT Water; two coupling groups - more accurate
tau_t= 0.2  0.2; time constant, in ps
ref_t= 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 5.0; 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
periodic_molecules = yes
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

--
Regards,
Dr. Neha S. Gandhi,


--

Message: 2
Date: Sun, 8 Oct 2017 22:34:21 +0530
From: Dilip H N 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding charges for atoms in a molecule
Message-ID:
 
Content-Type: text/plain; charset="UTF-8"

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
abc.gro command.
1] In the topology file, the charges for each atom are assigned. from where
are these charges assigned..?? is it from the .rtp file, itp file..??

2] If so, I compared the charges in the generated topology file and in the
merged.rtp file, but the cha

[gmx-users] Equilibration using position restraints in NPT

[Neha Gandhi]

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?





> Message: 1
> Date: Sun, 8 Oct 2017 23:38:58 +1000
> From: Neha Gandhi 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title= OPLS Lysozyme NPT equilibration
> define= -DPOSRES_CNT; position restrain the protein
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 50; 2
> dt= 0.001; 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
> ;energygrps   = Protein  CNT Water NA
> ; 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
> cutoff-scheme   = Verlet
> ns_type= grid; search neighboring grid cells
> nstlist= 10; 20 fs, largely irrelevant with Verlet
> scheme
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; 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= Berendsen; modified Berendsen
> thermostat
> tc-grps= CNT Water; two coupling groups - more accurate
> tau_t= 0.2  0.2; time constant, in ps
> ref_t= 310   310   ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Berendsen; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box
> vectors
> tau_p= 5.0; 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
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
>
>
> --
>
> Message: 2
> Date: Sun, 8 Oct 2017 22:34:21 +0530
> From: Dilip H N 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Regarding charges for atoms in a molecule
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
> ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
> abc.gro command.
> 1] In the topology file, the charges for each atom are assigned. from where
> are these charges assigned..?? is it from the .rtp file, itp file..??
>
> 2] If so, I compared the charges in the generated topology file and in the
> merged.rtp file, but the charges are different in both the files...
>
> 3] I even checked in the ffnonbonded.itp file, but here for all the atom
> types the charges a

Re: [gmx-users] Equilibration using position restraints in NPT

[Mark Abraham]

Hi,

The simplest explanation is that your box size is inappropriate for the
contents. If the box wants to change size but the nanotube is restrained to
fixed positions then you have an invalid model.

Mark

On Sun, 8 Oct 2017 15:39 Neha Gandhi  wrote:

> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title= OPLS Lysozyme NPT equilibration
> define= -DPOSRES_CNT; position restrain the protein
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 50; 2
> dt= 0.001; 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
> ;energygrps   = Protein  CNT Water NA
> ; 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
> cutoff-scheme   = Verlet
> ns_type= grid; search neighboring grid cells
> nstlist= 10; 20 fs, largely irrelevant with Verlet
> scheme
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; 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= Berendsen; modified Berendsen
> thermostat
> tc-grps= CNT Water; two coupling groups - more accurate
> tau_t= 0.2  0.2; time constant, in ps
> ref_t= 310   310   ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Berendsen; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box
> vectors
> tau_p= 5.0; 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
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> --
> 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.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Regarding charges for atoms in a molecule

[Justin Lemkul]

On 10/8/17 1:04 PM, Dilip H N wrote:

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
abc.gro command.
1] In the topology file, the charges for each atom are assigned. from where
are these charges assigned..?? is it from the .rtp file, itp file..??


Charges are in the .rtp file (see the manual for how pdb2gmx works).


2] If so, I compared the charges in the generated topology file and in the
merged.rtp file, but the charges are different in both the files...


If you have just a single glycine, and you applied N- and C-terminal 
patches to it, the residue is modified according to the .n.tdb and 
.c.tdb entries. This is probably where the differences lie.



3] I even checked in the ffnonbonded.itp file, but here for all the atom
types the charges are 0.00 only...(why is this so...??)


Because those charges are never used for anything and have no meaning.


So, from where (or) where are the charges specified..in which file


The "real" answer is that they are derived by those of us who work very 
hard to parametrize force fields, and you can get information on how 
that was done by reading the appropriate literature. This is really 
important to do so you understand how the force field works, pros and 
cons, etc. The implementation of charges into various files is just a 
technical detail.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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[gmx-users] Regarding charges for atoms in a molecule

[Dilip H N]

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
abc.gro command.
1] In the topology file, the charges for each atom are assigned. from where
are these charges assigned..?? is it from the .rtp file, itp file..??

2] If so, I compared the charges in the generated topology file and in the
merged.rtp file, but the charges are different in both the files...

3] I even checked in the ffnonbonded.itp file, but here for all the atom
types the charges are 0.00 only...(why is this so...??)

So, from where (or) where are the charges specified..in which file

Any suggestions are appreciated...


-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Equilibration using position restraints in NPT

[Neha Gandhi]

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title= OPLS Lysozyme NPT equilibration
define= -DPOSRES_CNT; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2
dt= 0.001; 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
;energygrps   = Protein  CNT Water NA
; 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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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= Berendsen; modified Berendsen thermostat
tc-grps= CNT Water; two coupling groups - more accurate
tau_t= 0.2  0.2; time constant, in ps
ref_t= 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 5.0; 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
periodic_molecules = yes
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

-- 
Regards,
Dr. Neha S. Gandhi,
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Re: [gmx-users] Switching off electorstaic

[David van der Spoel]

On 08/10/17 04:12, atanu das wrote:

Hi,
I am intending to run a simulation of a protein in 100 nM NaCl solution by 
turning off protein's electrostatic interactions, but keeping the LJ alive, so 
that water and salt behave as usual and the protein only behaves as a 
hydrophobic polymer chain. The most obvious way that I could think of is 
editing the topol.top file and setting the partial charges of all the protein 
atoms to be zero. However, I am slightly skeptical about using such a crude 
method. Is there any better way to turn off the electrostatics of the protein 
only?
ThanksAtanu

You may want to slowly turn of the charges using free energy code 
although it will be slower. Of course even a hydrophobic chain has 
charges, and doing what you plan to will mess up the balance between 
Coulomb and Lennard-Jones interaction. You may get some insight but 
nothing of physical relevance that you can compare to any experiment.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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