Re: [gmx-users] MnO2 periodic system

[Dallas Warren]

What do you mean "deformed"?

The "deformation" that you have encountered is probably most likely
due to the topology, rather than the simulation settings (since you
have constant volume set).  So that means there are issues with your
topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 5 August 2017 at 02:51, gangotri dey  wrote:
> Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster periodic). After the
> NVT run, I see that the surface is deformed. I was wondering what else can
> I add in my nvt.mdp to not encounter this problem?
>
> I have mainly followed the examples in the forum for graphene/CNT growth.
>
> title   = MnO2  in H2O NVT equilibration
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 50 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 50; save coordinates every 0.10 ps
> nstvout = 50; save velocities every 0.10 ps
> nstenergy   = 50; save energies every 0.10 ps
> nstlog  = 50; update log file every 0.10 ps
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen thermostat
> tc-grps = SOL MnO ; three 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 is off
> pcoupl  = no; no pressure coupling in NVT
> ; 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 = yes   ; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= 18; generate a random seed
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> --
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Re: [gmx-users] [gmx-developers] importing amber parameters to gromacs format?

[Justin Lemkul]

On 8/7/17 2:47 PM, Ming wrote:


  Hi gromacs team,

I am trying to simulate a protein ligand complex using gromacs, where I have two 
manganese ions bound with the ligand. I searched the gromacs force field and 
there was no parameter data for Mn. After some research online I found the 
following Amber link that has Mn parameters. Some online constructions says 
ffamber ports can do the work, but there were no more detailed instructions. I 
don't have much experiences converting amber parameters to files that gromacs 
can recognize, so I want to see if anyone here can help me on this by giving me 
some more detailed instructions?




Please ask general usage questions on the gmx-users mailing list.  I am CCing 
this message there and ask that any further questions be posted there. 
gmx-developers is for discussion of code and development.


This is just a unit/format conversion issue.  The AMBER manual will (should) 
describe the format of its force field files, and the GROMACS manual describes 
its required format.  Beyond syntax of the files, it's just a matter of 
converting kcal -> kJ and A -> nm, and maybe computing LJ parameters if the 
AMBER specification differs from that of GROMACS (sigma and epsilon).


-Justin

--
==

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] (no subject)

[Alex]

I did not quite understand your comment.

However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.

G


There are a few points to be made...
1. The shape of your system, which is "solvated in all 3 directions" is 
very unclear. Is this a brick floating in water?
2. Please do not solvate anything until you have established that your 
"surface" is happy in vacuum.
3. If you have bending as a whole, it could be indicative of large 
internal strains, in which case NVT is probably a poor option. When you 
say you have "a surface MnO2 model," is it something like this? 
https://upload.wikimedia.org/wikipedia/commons/8/81/Manganese-dioxide-from-xtal-sheet-3D-balls.png
4. This community is mostly focused on biomolecular simulations and 
noone will be able to verify your parameterization of a solid crystal. 
Here is the rule of thumb though: If something bends when it shouldn't 
bend, your model is bad, which really has nothing to do with Gromacs.
5. If you are a student and points 1-4 aren't something your doctoral 
advisor already mentioned, maybe you should find another advisor.


Alex


Hi,

Are you trying to implement a model that you know is capable of produce a
surface that does not deform in unexpected ways?

Mark

On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:


Dear all,

I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can

I

add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT

growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen

thermostat

tc-grps = SOL MnO ; three 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 is off
pcoupl  = no; no pressure coupling in NVT
; 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 = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
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* Please 

Re: [gmx-users] Memory issues using -ac option of gmx hbond

[Mark Abraham]

Hi,

To diagnose such issues, explore using fewer frames and more restrictive
selections for the analysis.

Mark

On Mon, 7 Aug 2017 23:55 Smith, Micholas D.  wrote:

> I had a similar problem. Using gromacs 2016.3's hbond tool fixed this.
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Jared
> Sagendorf 
> Sent: Monday, August 07, 2017 5:46 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Memory issues using -ac option of gmx hbond
>
> I'm trying to analyzing hydrogen bonds between a DNA and protein complex.
> When using the -ac option of gmx hbond, I'm getting segmentation faults
> which look like an out-of-memory problem.
>
> However, I'm giving the process 64gb of memory, and an additional 64gb of
> virtual memory. How memory intenstive is this program??
>
> Note I am using version 5.1.13. A snippet of the output is below
>
> Calculating hydrogen bonds between DNA_interface (919 atoms) and
> Protein_interface (1026 atoms)
> Found 138 donors and 458 acceptors
> Making hbmap structure...done.
> ...
> Found 117 different hydrogen bonds in trajectory
> Found 156 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> - Reduced number of hbonds from 117 to 116
> - Reduced number of distances from 156 to 156
> Average number of hbonds per timeframe 16.544 out of 31602 possible
>
>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
> Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
> J. Phys. Chem. B 110 (2006) pp. 4393-4398
>   --- Thank You ---  
>
> Doing autocorrelation according to the theory of Luzar and Chandler.
> [hpc3338:34436] *** Process received signal ***
> [hpc3338:34436] Signal: Segmentation fault (11)
> [hpc3338:34436] Signal code: Address not mapped (1)
> [hpc3338:34436] Failing at address: 0xfde7c370
> [hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370]
> [hpc3338:34436] [ 1]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x464449)[0x7ff5c4a7b449]
> [hpc3338:34436] [ 2]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(cross_corr+0x39)[0x7ff5c4a7b019]
> [hpc3338:34436] [ 3]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x339bb2)[0x7ff5c4950bb2]
> [hpc3338:34436] [ 4]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(gmx_hbond+0x312e)[0x7ff5c4947aae]
> [hpc3338:34436] [ 5]
>
> /usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x7ff5c47b4637]
> [hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea]
> [hpc3338:34436] [ 7]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff5c2c01b35]
> [hpc3338:34436] [ 8] gmx_mpi[0x40be69]
> [hpc3338:34436] *** End of error message ***
>
>
> Am I doing something wrong here?
> --
> Gromacs Users mailing list
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

On the information given, nobody can tell whether the parameters you have
for the interactions between Mn and O and maybe water are unsuitable, or
that something is wrong with the method, or the initial conditions, or the
code.

Mark

On Mon, 7 Aug 2017 23:11 gangotri dey  wrote:

> I did not quite understand your comment.
>
> However, I am trying my best to answer it.
> I have a surface MnO2 model. I have solvated the structure in all 3
> directions. After that, I minimize it and run NVT simulation with the
> parameters as mentioned. However, I see that there is a deformation of the
> surface and it does not remain a flat surface. Instead, it curls like a
> ribbon. This should not be the case. Hence, I am wondering what are the
> factors that can lead to this deformation? Are the parameters in the NVT
> simulation good enough or else there is a problem that I cannot see.
>
> G
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
>
>
>
>
> On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Are you trying to implement a model that you know is capable of produce a
> > surface that does not deform in unexpected ways?
> >
> > Mark
> >
> > On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
> >
> > > Dear all,
> > >
> > > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> > > have solvated the surface with water in all 3 directions. After the NVT
> > > run, I see that the surface is deformed. I was wondering what else can
> I
> > > add in my nvt.mdp to not encounter this problem?
> > >
> > > I have mainly followed the examples in the forum for graphene/CNT
> growth.
> > >
> > > title   = MnO2  in H2O NVT equilibration
> > > ; Run parameters
> > > integrator  = md; leap-frog integrator
> > > nsteps  = 5 ; 2 * 50 = 100 ps
> > > dt  = 0.002 ; 2 fs
> > > ; Output control
> > > nstxout = 50; save coordinates every 0.10 ps
> > > nstvout = 50; save velocities every 0.10 ps
> > > nstenergy   = 50; save energies every 0.10 ps
> > > nstlog  = 50; update log file every 0.10 ps
> > > ; Bond parameters
> > > continuation= no; first dynamics run
> > > constraint_algorithm= lincs ; holonomic constraints
> > > constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen
> > thermostat
> > > tc-grps = SOL MnO ; three 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 is off
> > > pcoupl  = no; no pressure coupling in NVT
> > > ; 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 = yes   ; assign velocities from Maxwell
> > > distribution
> > > gen_temp= 300   ; temperature for Maxwell distribution
> > > gen_seed= 18; generate a random seed
> > >
> > >
> > > *Thank you*
> > >
> > > *Gangotri Dey*
> > > Postdoctoral Associate
> > > Rutgers University New Brunswick
> > > Chemistry and Chemical Biology
> > > 174 Frelinghuysen Road, Piscataway, NJ 08854
> > > Phone: +16092162254
> > > --
> > > 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
> > > 

[gmx-users] Memory issues using -ac option of gmx hbond

[Jared Sagendorf]

I'm trying to analyzing hydrogen bonds between a DNA and protein complex.
When using the -ac option of gmx hbond, I'm getting segmentation faults
which look like an out-of-memory problem.

However, I'm giving the process 64gb of memory, and an additional 64gb of
virtual memory. How memory intenstive is this program??

Note I am using version 5.1.13. A snippet of the output is below

Calculating hydrogen bonds between DNA_interface (919 atoms) and
Protein_interface (1026 atoms)
Found 138 donors and 458 acceptors
Making hbmap structure...done.
...
Found 117 different hydrogen bonds in trajectory
Found 156 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 117 to 116
- Reduced number of distances from 156 to 156
Average number of hbonds per timeframe 16.544 out of 31602 possible

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
  --- Thank You ---  

Doing autocorrelation according to the theory of Luzar and Chandler.
[hpc3338:34436] *** Process received signal ***
[hpc3338:34436] Signal: Segmentation fault (11)
[hpc3338:34436] Signal code: Address not mapped (1)
[hpc3338:34436] Failing at address: 0xfde7c370
[hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370]
[hpc3338:34436] [ 1]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x464449)[0x7ff5c4a7b449]
[hpc3338:34436] [ 2]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(cross_corr+0x39)[0x7ff5c4a7b019]
[hpc3338:34436] [ 3]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x339bb2)[0x7ff5c4950bb2]
[hpc3338:34436] [ 4]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(gmx_hbond+0x312e)[0x7ff5c4947aae]
[hpc3338:34436] [ 5]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x7ff5c47b4637]
[hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea]
[hpc3338:34436] [ 7]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff5c2c01b35]
[hpc3338:34436] [ 8] gmx_mpi[0x40be69]
[hpc3338:34436] *** End of error message ***


Am I doing something wrong here?
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Re: [gmx-users] (no subject)

[gangotri dey]

I did not quite understand your comment.

However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.

G



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham 
wrote:

> Hi,
>
> Are you trying to implement a model that you know is capable of produce a
> surface that does not deform in unexpected ways?
>
> Mark
>
> On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
>
> > Dear all,
> >
> > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> > have solvated the surface with water in all 3 directions. After the NVT
> > run, I see that the surface is deformed. I was wondering what else can I
> > add in my nvt.mdp to not encounter this problem?
> >
> > I have mainly followed the examples in the forum for graphene/CNT growth.
> >
> > title   = MnO2  in H2O NVT equilibration
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 5 ; 2 * 50 = 100 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 50; save coordinates every 0.10 ps
> > nstvout = 50; save velocities every 0.10 ps
> > nstenergy   = 50; save energies every 0.10 ps
> > nstlog  = 50; update log file every 0.10 ps
> > ; Bond parameters
> > continuation= no; first dynamics run
> > constraint_algorithm= lincs ; holonomic constraints
> > constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen
> thermostat
> > tc-grps = SOL MnO ; three 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 is off
> > pcoupl  = no; no pressure coupling in NVT
> > ; 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 = yes   ; assign velocities from Maxwell
> > distribution
> > gen_temp= 300   ; temperature for Maxwell distribution
> > gen_seed= 18; generate a random seed
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > Postdoctoral Associate
> > Rutgers University New Brunswick
> > Chemistry and Chemical Biology
> > 174 Frelinghuysen Road, Piscataway, NJ 08854
> > Phone: +16092162254
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] time calculations

[Mark Abraham]

Hi,

I can't tell what question you're asking. Can you rephrase it please?

Mark

On Mon, 7 Aug 2017 08:05 faru honey  wrote:

> Please any one tell me that on what basis the time calculations occurs
> that is in pico seconds
>
>
> Sent from Mail for Windows 10
>
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Are you trying to implement a model that you know is capable of produce a
surface that does not deform in unexpected ways?

Mark

On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:

> Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> have solvated the surface with water in all 3 directions. After the NVT
> run, I see that the surface is deformed. I was wondering what else can I
> add in my nvt.mdp to not encounter this problem?
>
> I have mainly followed the examples in the forum for graphene/CNT growth.
>
> title   = MnO2  in H2O NVT equilibration
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 50 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 50; save coordinates every 0.10 ps
> nstvout = 50; save velocities every 0.10 ps
> nstenergy   = 50; save energies every 0.10 ps
> nstlog  = 50; update log file every 0.10 ps
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen thermostat
> tc-grps = SOL MnO ; three 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 is off
> pcoupl  = no; no pressure coupling in NVT
> ; 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 = yes   ; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= 18; generate a random seed
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
> --
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Re: [gmx-users] solvate only in the z-direction

[Mark Abraham]

Solvate everything and then delete all molecules that have any
inappropriate z coordinate. Or make a box whose lowest z coordinate is what
you want, solvate that, and then add your surface below that.

Mark

On Mon, 7 Aug 2017 22:33 gangotri dey  wrote:

> Dear all,
>
> I am working with MnO2 surface and I would like to solvate the surface only
> in the z-direction. How best can I do it, please?
>
> *Thank you*
>
> *Gangotri Dey*
> --
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Re: [gmx-users] clayff forcefield

[Mark Abraham]

Hi,

Didn't someone already answer that you need to make a forcefield folder, eg
in your working directory? You will need to follow the examples in the
gromacs version you are using to name things appropriately.

Mark

On Mon, 7 Aug 2017 22:54 G R  wrote:

> Dear usres,
>
> I try to write clayff forcefield, and I want to simulate Kaolinite. I have
> some questions about it.
> 1) should I write clayff forcefield separately or modify one of the
> forcefields in share/top?
> 2) The directory for clayff forcefield should be included ffbonded.itp,
> ffnonbonded.itp, atomname2type.n2t, forcefield.itp,
> forcefield.doc,atomtype.atp? if it is needed any other file please let me
> know?
> 3) In .n2t file, the first column should be written corresponding .gro
> file?
> 4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and
> oh (oxygen in hydroxyl group). Am I right?
>
> Any help will be appreciated,
> Golnaz
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[gmx-users] clayff forcefield

[G R]

Dear usres,

I try to write clayff forcefield, and I want to simulate Kaolinite. I have
some questions about it.
1) should I write clayff forcefield separately or modify one of the
forcefields in share/top?
2) The directory for clayff forcefield should be included ffbonded.itp,
ffnonbonded.itp, atomname2type.n2t, forcefield.itp,
forcefield.doc,atomtype.atp? if it is needed any other file please let me
know?
3) In .n2t file, the first column should be written corresponding .gro
file?
4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and
oh (oxygen in hydroxyl group). Am I right?

Any help will be appreciated,
Golnaz
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[gmx-users] solvate only in the z-direction

[gangotri dey]

Dear all,

I am working with MnO2 surface and I would like to solvate the surface only
in the z-direction. How best can I do it, please?

*Thank you*

*Gangotri Dey*
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Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

[Maghesree Chakraborty]

Thank you for your response. I did not have tabulated potentials for bonded
interactions. I had tabulated potentials only for non-bonded
interactions. I had set constraints to be all-angles in my mdp file. I will
try using "constraint" interaction explicitly in my topology instead of
converting bonds and angles into constraints via mdp directive.

On Mon, Aug 7, 2017 at 1:58 PM, Mark Abraham 
wrote:

> Hi,
>
> Tabulated bonded interactions are the opposite of constraints. You can
> explicitly use a "constraint" interaction type in your topology, which
> sounds like a good start. See chapter five of the reference manual.
>
> Mark
>
> On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty 
> wrote:
>
> > Hello,
> >
> > I am trying to run a CG simulation with only non-bonded interactions. I
> > have obtained the tabulated potentials for those interactions by
> > force-matching using VOTCA. I want all my bonds and angles to be
> > constrained as they are in the initial cg_conf.gro file. Since I do not
> > have tabulated potentials for bonded interactions, gromacs gives error
> if I
> > do not provide the bond and angle parameters (b0,kb and θ0 , kθ) in the
> > topology file. Then I tried setting the bond parameter (b0) to be the
> mean
> > of bond-length distribution in cg_conf.gro and the angle parameter (θ0)
> to
> > be the mean of the angle distribution in cg_conf.gro, I constrain the
> bonds
> > and angles with LINCS in my grompp file. During simulation, I get a lot
> of
> > LINCS warning and simulation is aborted. I am wondering if there is a way
> > of constraining the initial configurations of the molecules as they are
> in
> > cg_conf.gro file  in the absence of tabulated bonded potentials and not
> > forcing the molecules to have the bond-lengths and angles as specified
> by
> > the topology parameters.
> >
> > Thank you.
> >
> > Regards,
> > M. Chakraborty
> > --
> > Gromacs Users mailing list
> >
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Re: [gmx-users] Non Standard residues moving Away

[Justin Lemkul]

On 8/7/17 3:01 PM, Souvik Dey wrote:

Hi,

Grompp is running successfully without any errors. But my protein and
ligands are very far away from each other. So, what I fear is that the
interactions among them may not be well accounted for by MD simulations.



If the coordinates that came out of your topology generation program are 
incorrect, then it is pointless to use them.  Use the original coordinates from 
the bound complex.  No sense wasting time with a fruitless simulation when you 
already had usable coordinates.


-Justin


On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham 
wrote:


Hi,

The only thing that matters is the order of the molecules, residues and
atoms, and preferably naming. These must match between topology and
coordinates when you eg use grompp. The point of doing an MD simulation is
generally to keep the topology constant while changing the coordinates. So
give grompp whatever file in whatever format suits you, subject to the
above constraint.

Mark

On Mon, 7 Aug 2017 16:25 Souvik Dey  wrote:


Hi,

I am trying to simulate a Protein Ligand system. Now, my system has some
non standard residues and I standardized them for AMBER forcefield using
ACPYPE. However, when I assemble the gro files of the Proten generated

from

pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
situated next to each other. They have have moved far away.

Now, is there any trick by which the coordinates of the PDB file do not
change while being converted into a gro file or is there any way to

restore

the previous condition of the PDB file?

Thanking you,
Souvik Dey

--
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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--
==

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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Re: [gmx-users] Non Standard residues moving Away

[Souvik Dey]

Hi,

Grompp is running successfully without any errors. But my protein and
ligands are very far away from each other. So, what I fear is that the
interactions among them may not be well accounted for by MD simulations.

On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham 
wrote:

> Hi,
>
> The only thing that matters is the order of the molecules, residues and
> atoms, and preferably naming. These must match between topology and
> coordinates when you eg use grompp. The point of doing an MD simulation is
> generally to keep the topology constant while changing the coordinates. So
> give grompp whatever file in whatever format suits you, subject to the
> above constraint.
>
> Mark
>
> On Mon, 7 Aug 2017 16:25 Souvik Dey  wrote:
>
> > Hi,
> >
> > I am trying to simulate a Protein Ligand system. Now, my system has some
> > non standard residues and I standardized them for AMBER forcefield using
> > ACPYPE. However, when I assemble the gro files of the Proten generated
> from
> > pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
> > situated next to each other. They have have moved far away.
> >
> > Now, is there any trick by which the coordinates of the PDB file do not
> > change while being converted into a gro file or is there any way to
> restore
> > the previous condition of the PDB file?
> >
> > Thanking you,
> > Souvik Dey
> >
> > --
> > Souvik Dey
> > Integrated Science Education & Research Centre
> > Visva Bharati University
> > Santiniketan-731235
> > West Bengal
> > 8981736643
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

[Mark Abraham]

Hi,

Tabulated bonded interactions are the opposite of constraints. You can
explicitly use a "constraint" interaction type in your topology, which
sounds like a good start. See chapter five of the reference manual.

Mark

On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty 
wrote:

> Hello,
>
> I am trying to run a CG simulation with only non-bonded interactions. I
> have obtained the tabulated potentials for those interactions by
> force-matching using VOTCA. I want all my bonds and angles to be
> constrained as they are in the initial cg_conf.gro file. Since I do not
> have tabulated potentials for bonded interactions, gromacs gives error if I
> do not provide the bond and angle parameters (b0,kb and θ0 , kθ) in the
> topology file. Then I tried setting the bond parameter (b0) to be the mean
> of bond-length distribution in cg_conf.gro and the angle parameter (θ0) to
> be the mean of the angle distribution in cg_conf.gro, I constrain the bonds
> and angles with LINCS in my grompp file. During simulation, I get a lot of
> LINCS warning and simulation is aborted. I am wondering if there is a way
> of constraining the initial configurations of the molecules as they are in
> cg_conf.gro file  in the absence of tabulated bonded potentials and not
> forcing the molecules to have the bond-lengths and angles as specified  by
> the topology parameters.
>
> Thank you.
>
> Regards,
> M. Chakraborty
> --
> Gromacs Users mailing list
>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] How to Identify clusters

[Mark Abraham]

Hi,

The gromacs documentation pages list all the analysis programs available,
along with a summary of what they can do. Each tool has its own
documentation, too. Exploring that will tend to get you a useful answer
sooner than emailing! Or at least a more focussed question.

Mark

On Sun, 6 Aug 2017 16:54 Sameer Edirisinghe  wrote:

> Dear all,
>
> I need to identify clusters in my polymer system. I have 200ns simulation
> trajectory and using this how can I identify the clusters existing in my
> system over the time? Need to find which molecules form the cluster. Can
> anyone suggest a method to do this?
>
>
> Regards
> Bhagya Karunarathna
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Re: [gmx-users] Non Standard residues moving Away

[Mark Abraham]

Hi,

The only thing that matters is the order of the molecules, residues and
atoms, and preferably naming. These must match between topology and
coordinates when you eg use grompp. The point of doing an MD simulation is
generally to keep the topology constant while changing the coordinates. So
give grompp whatever file in whatever format suits you, subject to the
above constraint.

Mark

On Mon, 7 Aug 2017 16:25 Souvik Dey  wrote:

> Hi,
>
> I am trying to simulate a Protein Ligand system. Now, my system has some
> non standard residues and I standardized them for AMBER forcefield using
> ACPYPE. However, when I assemble the gro files of the Proten generated from
> pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
> situated next to each other. They have have moved far away.
>
> Now, is there any trick by which the coordinates of the PDB file do not
> change while being converted into a gro file or is there any way to restore
> the previous condition of the PDB file?
>
> Thanking you,
> Souvik Dey
>
> --
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> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
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Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv

[Neda Rafiee]

Thanks a lot Justin
Neda


- Original Message -
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Sent: Mon, 07 Aug 2017 19:08:05 +0430 (IRDT)
Subject: Re: [gmx-users] converting xtc to pdb without need to tpr file using 
trjconv



On 8/7/17 2:42 AM, Neda Rafiee wrote:
> Dear users,
> Anyone knows how can I use trjconv to convert an xtc file to pdb format 
> without need to tpr file ?

trjconv does accept PDB files to -s but then you don't get PBC or connectivity 
information.  You need to provide some source of atom and residue names, 
because 
none of that is in an XTC file.

-Justin

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Re: [gmx-users] Performance values

[Maureen Chew]

Szilárd,
Thank you so very much for the reply!You mention
that time/step is important if trying to do an apples-to-apples
comparison for any given simulation.

I have a few questions - For specific example, use the RNAse reference here:
(http://www.gromacs.org/gpu )
Influence of box geometry and virtual interaction sites
This is a simulation of the protein RNAse, which contains roughly 24,000 atoms 
in a cubic box.
The image rnase.png , 
shows a 6 core baseline to be, roughly 50ns/day

First,  assuming this is from rnase_cubic @ 
ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz 

which contains these files:
rnase_cubic/rf_verlet.mdp
rnase_cubic/conf.gro
rnase_cubic/topol.top
rnase_cubic/pme_verlet.mdp

3 questions:
- What gmx grompp command was use to generate the tpr file for the result in 
rnase.png?
Apologies if its intuitively obvious which mdp  was used
- Aside from -ntmpi and -ntomp parms, what gmx mdrun command was used to obtain
the 6 core result?
- From that 6 core run, what is the time/step that you refer to?  Is that
real cycle  and time accounting for neighbor search, force, PME mesh 
etc,
and  time/step that you refer to is the wall time/call count?

Thanks in advance!
—maureen


Date: Mon, 7 Aug 2017 16:01:16 +0200
From: Szilárd Páll >
To: Discussion list for GROMACS users >
Subject: Re: [gmx-users] Performance values


Indeed, "Wall t" is real application wall-time, nanoseconds/day is the
typical molecular dynamics performance unit that corresponds to the
effective amount of simulation throughput (note that this however
depends on the time-step and without that specified it is not useful
to compare to other runs), so often it is useful to use it convert it
to time/step.
--
Szilárd


On Fri, Jul 28, 2017 at 10:20 AM, Maureen Chew > wrote:
> You might find this reference handy - it has a really nice explanation for 
> how to look
> at a log file
> Topology preparation, "What's in a log file", basic performance improvements: 
> Mark Abraham, Session 1A 
>   
> >
> 
> The ?Performance:? values are a throughput measure where both values represent
> the same thing in different terms.  In your sample below, 3.964 is the
> number of nanoseconds that can be simulated in 24 hours while it takes
> 6.054 hours to simulate 1 ns
> 
> HTH
> 
> 
> On Jul 27, 2017, at 10:15 AM, Maureen Chew  > wrote:
>> Where is it documented how the mdrun performance metrics are calculated ? 
>> I?ve
>> looked here
>> http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
>>  
>> 
>>  
>> >  
>> >
>> and here
>> http://manual.gromacs.org/documentation/2016.3/manual-2016.3.pdf 
>>  
>> > >
>> 
>> but seem to have missed  explanation.
>> 
>> Are the sample mdrun times below user time or real time?  Generally, wall is 
>> real time
>> I understand that ?Performance:? is not a linear scale but what is the scale
>> in the 2016.3 sample below?
>> 
>> Core t (s)   Wall t (s)(%)
>>  Time:69761.050  272.50425600.0
>>(ns/day)(hour/ns)
>> Performance:3.9646.054
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Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

[ZHANG Cheng]

Dear Yujie Liu,
Can I clarify your suggestions?


copy gly.gro into protein.gro and changed the number of atoms:
) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f 
protein_newbox.gro -o protein_glycine.gro",
the "protein_glycine.gro" already contains both protein residues and glycine 
ones, with 10 glycines following the proteins residues, as if they belong to a 
same molecule as shown below, so I can assume it is already copied as you 
suggested?


  (.. protein residues from 1 to 442)
  442ALAHB1 6611   2.350   3.446   6.215
  442ALAHB2 6612   2.294   3.373   6.080
  442ALAHB3 6613   2.225   3.341   6.225
  442ALA  C 6614   2.443   3.233   6.346
  442ALA OT 6615   2.357   3.205   6.425
  442ALA  O 6616   2.556   3.249   6.383
  442ALA HO 6617   2.561   3.236   6.483
  443GLY  N 6618   5.163   5.878   5.519
  443GLY H1 6619   5.235   5.930   5.475
  443GLY H2 6620   5.179   5.780   5.507
  443GLY H3 6621   5.075   5.902   5.479
  443GLY CA 6622   5.160   5.910   5.663
  443GLYHA1 6623   5.250   5.886   5.701
  443GLYHA2 6624   5.145   6.008   5.672
  443GLY  C 6625   5.052   5.834   5.736
  443GLY OT 6626   5.046   5.831   5.857
  443GLY  O 6627   4.965   5.774   5.662
  443GLY HO 6628   4.898   5.727   5.720
  (.. glycine molecules from 443 to 452)
  10.88213  10.88213  10.88213 (this is the dimension of the box)


-


Then using #include??  ?? lines to add gly.itp into protein.top in suitable 
position 
) Do you mean in the protein.top file, change


; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"
#endif


into


; Include Position restraint file
#ifdef POSRES
#include "posre_protein.itp"
#include "posre_gly.itp"
#endif


?


-
changed [molecules] options to add the name and number of gly molecule. Note 
the information of posre_gly.itp.
) Do you mean in the protein.top file, change


[ molecules ]
; Compound#mols
Protein_chain_L 1


into


[ molecules ]
; Compound#mols
Protein_chain_L 1   (the "Protein_chain_L" refers to the protein)
Protein 10  (the "Protein" refers to the glycine)


?





-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Mon, Aug 7, 2017 07:34 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  How to configure the gro/itp/top files after running 
"insert-molecules"?



Dear Gromacs,
I am doing a MD for a protein with glycines.


For glycine, I use 
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got 
) gly.gro
) posre_gly.itp
) topol_gly.top


For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh 
-merge interactive
) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt 
cubic
and got
) protein_processed.gro
) posre_protein.itp
) topol_protein.top

) protein_newbox.gro


Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o 
protein_glycine.gro
and got
) protein_glycine.gro, in which the 10 glycines were appended to the protein 
residues, as if they belong to the same protein molecule (is this normal?)


Can I ask,
1) How can I configure the itp and top files (i.e. posre_gly.itp, 
topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD 
setting-up? E.g. should I combine them into one itp and one top file, how to do 
that?
2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy 
minimization. Is this the correct procedure?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv

[Justin Lemkul]

On 8/7/17 2:42 AM, Neda Rafiee wrote:

Dear users,
Anyone knows how can I use trjconv to convert an xtc file to pdb format without 
need to tpr file ?


trjconv does accept PDB files to -s but then you don't get PBC or connectivity 
information.  You need to provide some source of atom and residue names, because 
none of that is in an XTC file.


-Justin

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Re: [gmx-users] trans-membrane protein simulation

[Justin Lemkul]

On 8/6/17 10:25 PM, Amir Zeb wrote:

Hello gmx-users!

I want to simulate a membrane protein, where it sets across the membrane
(means that some of the protein's region lays outside the membrane and is
water exposed). Obviously, the protein will be experiencing two different
environments like membrane and water (heterogeneous condition) during the
simulation.

Will it please be recommended to follow the* Justin tutorial *for membrane
protein simulation (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
or I should make some modifications to this tutorial? Also, please suggest


In your case, don't center the protein to coincide with the center of the 
membrane (you'll have to figure out how it needs to be positioned).  The force 
field combination in that tutorial is also really outdated and better force 
fields exist.  The tutorial remains as is because it is a useful illustration of 
possible methods to build such systems and how force field files are organized. 
That doesn't mean you should do exactly as it does for your real scientific work.



me whether this kind of simulation in heterogeneous condition is worth
enough to get reliable data or not?


People do simulations like this all the time.  They generally need to be very 
long (hundreds of ns) to capture both protein and lipid dynamics.


-Justin

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Re: [gmx-users] Generating topology file for a long polymer chain

[Justin Lemkul]

On 8/6/17 8:35 PM, Mahsa E wrote:

Hello Justin,

Thank you so much for your reply!

I followed what you suggested. Please correct me if I misunderstood;

1- I used acpype to generate the parameters (charges, atom types, and
bonded parameters) for the monomer, which create many files including
GMX_OPLS.itp , GMX_OPLS.top and GMX.gro files.

2- Then I build the dimer and used the conformer search in Marvin/Avogadro
to find the best conformer for the dimer (.xyz or .pdb).



You'll need to parametrize (at minimum) dihedral terms around the bond 
connecting the monomers in the dimer.  Finding a single conformer doesn't give 
you that information.  You need to back up and consult the primary literature 
for how your force field should work and how things should be parametrized 
(right level of theory, expected level of agreement, etc).  This is not 
something that either acepype or GROMACS are going to give you; it usually 
requires QM work and parameter fitting.



3- The missing part for me is from this step. What should I do after
running acpype for the dimer ?
how to use the information from previous steps to generate the .itp file
for a longer chain of polymer (like 25 units)?



If you've parametrized all possible internal parameters in small model systems, 
there's nothing special about larger ones; they're just small model compounds 
linked together, so you've already done everything.  Just use pdb2gmx with 
suitable .rtp files:


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

-Justin

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[gmx-users] (no subject)

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can I
add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; 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= 1.0   ; 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  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL MnO ; three 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 is off
pcoupl  = no; no pressure coupling in NVT
; 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 = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
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Re: [gmx-users] Gmx hbond

[Justin Lemkul]

On 8/6/17 4:21 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have tc_groups = protein non-protein , it is best to consider protein and ligand as one single entity. So we use make-ndx to merg them. When i issue 


...for the purpose of thermostatting, nothing else.  Again, merging two groups 
doesn't eliminate either from the list unless you actually deleted them.


gmx hbond there isnt any ligand in this list to choose. How can i determine h 
bonds between protein and ligan , even in my project that is about HDAC2 and my 
designed drug


If you're working on a different system, you're not going to have the exact same 
options as in my tutorial.  Likely your ligand isn't called "JZ4," so look for 
something else that makes sense for your system.


-Justin


Thank you Farial



Sent from Yahoo Mail for iPhone


On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul  wrote:



On 8/4/17 11:13 AM, farial tavakoli wrote:

   blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, 
but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx 
make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs 
there anyone help me how to check the hydrogen bond of JZ4 ligand?


Both protein and ligand are default groups and do not require the use of an
index file.  If the ligand isn't showing up in the list, it's probably because
you're supplying an index file from which the ligand group has been deleted.

-Justin



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Re: [gmx-users] The small organic molecule occurred deformation during simulation

[Justin Lemkul]

On 8/5/17 2:59 PM, yujie liu wrote:


Mr Justin:

I have tried to do energy minimization in this situation which only existing 
small molecule in water, I found  the structure of organic molecule didn’t 
become distortions. I think  the distortions of organic molecules are due to 
these stronger interactions between small molecules and enzyme, because there 
is a enzyme molecule in the previous simulation. Do you think this 
consideration is correct? In the case, do you think this phenomenon  is normal? 
What’s more, I checked out the top file of small molecules and don’t find error 
and include the information of improper dihedrals.



Or your energy minimization simply indicates a strained initial structure that 
isn't fully relaxed.  Real MD sampling is important here; energy minimization 
won't tell the whole story, at least not in any reliable way.


-Justin

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Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

[Souvik Dey]

But what if the coordinates do not match? I mean Glycine may not have the
same coordinates after.

On Mon, Aug 7, 2017 at 2:48 PM, yujie liu  wrote:

>
> The .top file of protein has included itself all parameters, so now you
> only copy gly.gro into protein.gro and changed the number of atoms. Then
> using #include”  ” lines to add gly.itp into protein.top in suitable
> position and changed [molecules] options to add the name and number of gly
> molecule. Note the information of posre_gly.itp.
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Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
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[gmx-users] Non Standard residues moving Away

[Souvik Dey]

Hi,

I am trying to simulate a Protein Ligand system. Now, my system has some
non standard residues and I standardized them for AMBER forcefield using
ACPYPE. However, when I assemble the gro files of the Proten generated from
pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
situated next to each other. They have have moved far away.

Now, is there any trick by which the coordinates of the PDB file do not
change while being converted into a gro file or is there any way to restore
the previous condition of the PDB file?

Thanking you,
Souvik Dey

-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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Re: [gmx-users] Performance values

[Szilárd Páll]

Indeed, "Wall t" is real application wall-time, nanoseconds/day is the
typical molecular dynamics performance unit that corresponds to the
effective amount of simulation throughput (note that this however
depends on the time-step and without that specified it is not useful
to compare to other runs), so often it is useful to use it convert it
to time/step.
--
Szilárd


On Fri, Jul 28, 2017 at 10:20 AM, Maureen Chew  wrote:
> You might find this reference handy - it has a really nice explanation for 
> how to look
> at a log file
> Topology preparation, "What's in a log file", basic performance improvements: 
> Mark Abraham, Session 1A 
> 
>
> The “Performance:” values are a throughput measure where both values represent
> the same thing in different terms.  In your sample below, 3.964 is the
> number of nanoseconds that can be simulated in 24 hours while it takes
> 6.054 hours to simulate 1 ns
>
> HTH
>
>
> On Jul 27, 2017, at 10:15 AM, Maureen Chew  wrote:
>> Where is it documented how the mdrun performance metrics are calculated ? 
>> I?ve
>> looked here
>> http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
>>  
>> 
>> and here
>> http://manual.gromacs.org/documentation/2016.3/manual-2016.3.pdf 
>> 
>>
>> but seem to have missed  explanation.
>>
>> Are the sample mdrun times below user time or real time?  Generally, wall is 
>> real time
>> I understand that ?Performance:? is not a linear scale but what is the scale
>> in the 2016.3 sample below?
>>
>>  Core t (s)   Wall t (s)(%)
>>   Time:69761.050  272.50425600.0
>> (ns/day)(hour/ns)
>> Performance:3.9646.054
>>
>
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[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

[ZHANG Cheng]

Dear Gromacs,
I am doing a MD for a protein with glycines.


For glycine, I use 
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got 
) gly.gro
) posre_gly.itp
) topol_gly.top


For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh 
-merge interactive
) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt 
cubic
and got
) protein_processed.gro
) posre_protein.itp
) topol_protein.top

) protein_newbox.gro


Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o 
protein_glycine.gro
and got
) protein_glycine.gro, in which the 10 glycines were appended to the protein 
residues, as if they belong to the same protein molecule (is this normal?)


Can I ask,
1) How can I configure the itp and top files (i.e. posre_gly.itp, 
topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD 
setting-up? E.g. should I combine them into one itp and one top file, how to do 
that?
2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy 
minimization. Is this the correct procedure?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Visualization of xtc file

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi andrea
Thank you for replyYes i moved the speed control on the left but it wasnt 
affected. And now i went to graphical reprezentation and increased trajectory 
smoothing windows size but it was not ok too. It seems my protein has many 
aberrant bonds 

Sent from Yahoo Mail for iPhone


On Monday, August 7, 2017, 2:24 PM, Andrea Spitaleri  
wrote:

Hi

please refer to VMD guide/manual/mailing list. You have different 
options to "decrease" the motion:

1. in VMD Main there is a speed control, just move to left with mouse

or/and

2.  in Graphical Representations under Trajectory tab you can increase 
the number of "Trajectory Smoothing Window Size".

HTH

and


On 07/08/2017 11:38, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear gromacs user
> I am trying to view .gro and .xtc files of my complex by VMD but when i load 
> first .gro and then .xtc files in vmd , it has so high motion , such that no 
> molecules are viewable. Would you please help me how can i view it?
> ThanksFarial
>
>
> Sent from Yahoo Mail for iPhone
>  

-- 
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
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Re: [gmx-users] Visualization of xtc file

[Andrea Spitaleri]

Hi

please refer to VMD guide/manual/mailing list. You have different 
options to "decrease" the motion:


1. in VMD Main there is a speed control, just move to left with mouse

or/and

2.  in Graphical Representations under Trajectory tab you can increase 
the number of "Trajectory Smoothing Window Size".


HTH

and


On 07/08/2017 11:38, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am trying to view .gro and .xtc files of my complex by VMD but when i load 
first .gro and then .xtc files in vmd , it has so high motion , such that no 
molecules are viewable. Would you please help me how can i view it?
ThanksFarial


Sent from Yahoo Mail for iPhone
  


--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557

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[gmx-users] Visualization of xtc file

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs user
I am trying to view .gro and .xtc files of my complex by VMD but when i load 
first .gro and then .xtc files in vmd , it has so high motion , such that no 
molecules are viewable. Would you please help me how can i view it?
ThanksFarial


Sent from Yahoo Mail for iPhone
 
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[gmx-users] 2D maps

[Yasser Almeida Hernández]

Hello all,

I have CGMD simulation for a membrane protein embedded in a model 
membrane with several E. coli lipids, built with /insane/ script. I want 
to generate colored scaled 2D maps for the membrane thickness and for 
the lipids distributions for each bilayer leaflet. Could you give some 
guidelines in this regard?


Thanks in advance

Best regards

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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[gmx-users] amino acid adsorption on metal surface

[Rabia Mukhtar]

hello!
I am quiet beginner in Gromacs. I want to do adsorption of
tryptophan on Au(1 1 1) surface. Please help me that how can I construct
the gold surface in gromacs and how to adsorb tryptophan on that surface.

  Regards
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[gmx-users] converting xtc to pdb without need to tpr file using trjconv

[Neda Rafiee]

Dear users,
Anyone knows how can I use trjconv to convert an xtc file to pdb format without 
need to tpr file ? 
Thanks,
Neda
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[gmx-users] time calculations

[faru honey]

Please any one tell me that on what basis the time calculations occurs that is 
in pico seconds


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