[gmx-users] Convergence of systems.

[SHYANTANI MAITI]

Dear all,
How to  determine whether the system converges or not in molecular dynamics
simulation?

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*Shyantani Maiti*
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Re: [gmx-users] Convergence of systems.

[Quyen V. Vu]

there are various properties you can check such as potential energy, RMSD,
Temperature ...

On Thu, Jul 12, 2018 at 2:19 PM SHYANTANI MAITI 
wrote:

> Dear all,
> How to  determine whether the system converges or not in molecular dynamics
> simulation?
>
> --
> Best regards,
> *Shyantani Maiti*
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Re: [gmx-users] Convergence of systems.

[Dallas Warren]

What is important is whether that the property of interest to you has
stabilised into a particular state/value. What time frame that is depends
on the property of interest, temperature will stabilise relatively quickly,
within 1ns, volume can be longer, particularly if there is some
organisation required, but can be 10ns roughly. If organisation of
molecules is required, on a large scale, then you can easily be looked at
100ns, or even more.  And each of those values depends on the size of the
system, the later it is with more atoms present, the longer things will
take to stabilise.

And even once the property has stabilised, the eternal question is "if I
run it for a little longer, will it flip into a more stable state again?"
And can easily see that, something is stable for 10, 20, 50ns then suddenly
it flips into a more stable state.  How long is a piece of string?

Best idea is to monitor the property of interest, track it along the
simulation time. Run it for as long as it is still changing, then run for a
bit longer to ensure it has stabilised.

On Thu, 12 Jul. 2018, 5:19 pm SHYANTANI MAITI, 
wrote:

> Dear all,
> How to  determine whether the system converges or not in molecular dynamics
> simulation?
>
> --
> Best regards,
> *Shyantani Maiti*
> --
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[gmx-users] Membrane simulation analysis - membrane thickness and area per lipid

[Yasser Almeida Hernández]

Hello,

I am running some CGMD simulations of a membrane protein embedded in a 
model of E. coli membrane (12x12 nm bilayer with different lipids), and 
I want to do the analysis of the membrane thickness and area per lipid 
(APL). For these tasks I am comparing the performance of FATSLiM, 
APL@Voro, GridMAT-MD and the GROMACS tool densmap. For this I have 
several questions:


1 - I am running densmap as *gmx densmap -f traj.xtc -s topol.tpr -n 
PO4_index.ndx -od densmap.dat* selecting the lipid of interest (as the 
PO4 bead), previously grouped in the index file. Then I plotted the 
*densmap.dat* file in Origin, obtaining a color coded heatmap of each 
lipid for the upper and lower membrane leaflet. What are the unit for 
this density maps? The *-unit* options are in nm-3, nm-2 or count. If I 
select *-unit nm-2*, does that means number of lipids per nm-2?


2 - How different is the previous approach from the APL calculated in 
FATSLiM, APL@Voro, GridMAT-MD?


3 - Which is the best method for the membrane thickness calculation.

Thanks

Best

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] Dihedral between non bonded atoms

[Momin Ahmad]

Hi,

is there a reason why gromacs demands parameters for dihedral angles 
that are not bonded? For example i,j, and k are bonded but l is not. The 
distance of k and l is about 2.7 Angstroem. How can i tell gromacs to 
ignore these dihedrals during pdb2gmx. I did no define a bond in the 
.rtp file. The .pdb i used for pdb2gmx is attached.

Thanks in advance.

Cheers,
Momin

--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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[gmx-users] Time correlation function computation

[ABANTIKA PAL]

Dear All,

How to find time correlation function of the vectors formed by Cα of a protein 
in molecular dynamic simulation?

Thank You.

-Abantika
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Re: [gmx-users] Dihedral between non bonded atoms

[Mark Abraham]

Hi,

The list cannot accept attachments, so please find another way to share
your inputs, e.g. a file sharing service. The pdb on its own would not be
enough for anyone to help, because that doesn't tell us what atoms are
concerning you.

By design, pdb2gmx will not try to generate a dihedral if there's no
bond-like interaction in an .rtp building block, so I suspect the issue is
that there is a bond. Distance is not relevant.

Mark

On Thu, Jul 12, 2018 at 12:01 PM Momin Ahmad  wrote:

> Hi,
>
> is there a reason why gromacs demands parameters for dihedral angles
> that are not bonded? For example i,j, and k are bonded but l is not. The
> distance of k and l is about 2.7 Angstroem. How can i tell gromacs to
> ignore these dihedrals during pdb2gmx. I did no define a bond in the
> .rtp file. The .pdb i used for pdb2gmx is attached.
> Thanks in advance.
>
> Cheers,
> Momin
>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286 <+49%20721%2060824286>
> E-Mail: momin.ah...@kit.edu
>
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[gmx-users] Commented atoms in [pair] list

[Anjana Jayasinghe]

Dear Gromacs users,
Recently, I downloaded some simulation files from a web site (their work is 
already published). Once I checked their itp files, I saw that they commented 
some atoms in [pair] list. I would like to know what could be the reason for 
that?
Thank you. 
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[gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

[Raman Preet Singh]

Dear All,

I have earlier posted the below email but received no reply. I am reposting it 
and will be thankful if someone can help me out.

Regards,
Raman


On Jul 6, 2018 3:02 PM, Raman Preet Singh  wrote:
>
> Dear All,
>
>
> I want to run a CG simulation of carbon nanotubes (CNTs) and different 
> proteins. I have a few questions for which I request help:
>
>   1.
> Several groups have used CG models of CNTs, mapping 2, 2.5 or 3 carbons per 
> CG bead. I am a novice in CG models. Any help on creating CG models or 
> reference to a tutorial/website/paper/script will be appreciated.
>   2.
> VMD offers a residue-based CG which can convert the atomistic to CG structure 
> of proteins. Will it be OK to use this CG model of protein with CG model of 
> CNTs and perform simulation using MARTINI force field.
>
>
> Thank you in advance.
>
>
> Regards,
>
> Raman
>
>
>
> [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png]
>  Virus-free. 
> www.avg.com
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Re: [gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

[Peter Kroon]

Hi Raman,


I forwarded your question to some people off list, and chance has it I
just got a reply back! So with a big thanks to R. Alessandri and M. Vögele!


Peter



Hi,

1.) 
We made a tool to create Martini models for open carbon nanotubes: 
https://github.com/bio-phys/cnt-martini.
The parameters are described in the following paper:
http://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e
For closed/capped CNTs, check out the work by Luca Monticelli:
http://perso.ibcp.fr/luca.monticelli/MARTINI/index.html

2.) 
I have never used VMD for coarse-graining, but I would refrain from
using residue-based methods, as they are very specific for proteins and
will not work for other types of molecules.

Best regards,
Martin

-- 

Martin Vögele, M.Sc.
Max Planck Institute of Biophysics
Department of Theoretical Biophysics
Max-von-Laue-Str. 3
D-60438 Frankfurt am Main
Tel. +49 (0)69 / 6303 2505 


On 12-07-18 14:31, Raman Preet Singh wrote:
> Dear All,
>
> I have earlier posted the below email but received no reply. I am reposting 
> it and will be thankful if someone can help me out.
>
> Regards,
> Raman
>
>
> On Jul 6, 2018 3:02 PM, Raman Preet Singh  wrote:
>> Dear All,
>>
>>
>> I want to run a CG simulation of carbon nanotubes (CNTs) and different 
>> proteins. I have a few questions for which I request help:
>>
>>   1.
>> Several groups have used CG models of CNTs, mapping 2, 2.5 or 3 carbons per 
>> CG bead. I am a novice in CG models. Any help on creating CG models or 
>> reference to a tutorial/website/paper/script will be appreciated.
>>   2.
>> VMD offers a residue-based CG which can convert the atomistic to CG 
>> structure of proteins. Will it be OK to use this CG model of protein with CG 
>> model of CNTs and perform simulation using MARTINI force field.
>>
>>
>> Thank you in advance.
>>
>>
>> Regards,
>>
>> Raman
>>
>>
>>
>> [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png]
>>  Virus-free. 
>> www.avg.com
>> -- 
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>> mail to gmx-users-requ...@gromacs.org.


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Re: [gmx-users] GROMACS- suggestion for GPU buying

[Szilárd Páll]

If price does not matter, get V100s; if it matters somewhat get TITAN-V's.
Same applies if you want best performance per simulation. If you want best
perf/buck, the 1080 Ti is still better investment (or you could wait an see
if the next-gen consumer cards come out soon).

--
Szilárd


On Tue, Jul 10, 2018 at 4:12 PM malkeet singh Bahia 
wrote:

> Hello Developers!
> Hope you are doing well!
>
> We are interested in buying new GPU card for simulating relatively big
> protein systems (more than 300K atoms) using GROMACS latest version.
> Currently, we have one P100 card (with 16 "real" cpu cores) that provides a
> good speed of around 10 ns/day for that system size.
> We were wondering if there is any recommendation/experience with other
> cards that will speed up the simulation time. Specifically, V100 PCIE,
> TITAN-V ,or GTX-1080TI.
>
> Many thanks,
>
> Malkeet
> --
> Thanks & Warm Regards
>
> ​
> Malkeet S. Bahia, PhD
> Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
> PBC Indo-Israel Post-doc fellowship
> Dept. of Chemistry, Building 211, Room no. 211
> Bar Ilan University,  Ramat Gan, 5290002,  ISRAEL
>
> Mobile: +91-9815988501 (India, watts app only)
> +972-584553434 (Israel number)
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Re: [gmx-users] mpirun and gmx_mpi

[Szilárd Páll]

If you've written programs using MPI before you must know that you
generally use a launcher like mpirun/mpiexec or similar to start a run
(e.g. see https://www.open-mpi.org/doc/v1.10/man1/mpirun.1.php).

What is the confusion?

--
Szilárd


On Wed, Jul 11, 2018 at 9:16 AM Mahmood Naderan 
wrote:

> Hi,Although I have read the manual and I have wrote programs with mpi, the
> gromacs use of mpi is confusing.
> Is it mandatory to use mpirun before gmx_mpi or not?
> Can someone shed a light on that?
>
> Regards,
> Mahmood
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Re: [gmx-users] cpu threads in a gpu run

[Szilárd Páll]

On Mon, Jul 9, 2018 at 12:43 PM Mahmood Naderan 
wrote:

> Hi,
> When I run "-nt 16 -nb cpu", I see nearly 1600% cpu utilization.


You request the CPU to do the work, so all cores are fully utilized.


> However, when I run "-nt 16 -nb gpu", I see about 600% cpu utilization.


The default behavior is to offload if there is a GPU and if your GPU is not
fast enough to finish the work offloaded by default, you'll have imbalance
and the CPU will wait.


> Is there any reason about that? I want to know with the cpu threads in a
> gpu run is controllable.
>

See the documentation.



>
>
> Regards,
> Mahmood
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Re: [gmx-users] cpu threads in a gpu run

[Szilárd Páll]

On Tue, Jul 10, 2018 at 5:12 AM Mahmood Naderan 
wrote:

> No idea? It seems to be odd. At the beginning of run, I see
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>   application clocks of the detected Quadro M2000 GPU to improve
> performance.
>   Recompile with the NVML library (compatible with the driver used) or
> set application clocks manually.
>
>
> Is the behavior I see, related to this note? I doubt, but if someone has a
> comment, I appreciate that.
>
>
No, that just notes that the so-called "Application clocks" feature of
NVIDIA GPUs can be used to set a higher than default clock rate on the GPU
which in the majority of the cases improves performance.


>
> Regards,
> Mahmood
>
> On Monday, July 9, 2018, 3:13:20 PM GMT+4:30, Mahmood Naderan <
> nt_mahm...@yahoo.com> wrote:
>
>  Hi,
> When I run "-nt 16 -nb cpu", I see nearly 1600% cpu utilization. However,
> when I run "-nt 16 -nb gpu", I see about 600% cpu utilization. Is there any
> reason about that? I want to know with the cpu threads in a gpu run is
> controllable.
>
>
> Regards,
> Mahmood
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Re: [gmx-users] pme grid with gpu

[Szilárd Páll]

That's the PP-PME load balancing output (see -tunepme option /
http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.html
).


--
Szilárd


On Tue, Jul 10, 2018 at 7:35 PM Mahmood Naderan 
wrote:

> Hi,
> When I run mdrun with "-nb gpu", I see the following output
>
>
> starting mdrun 'Protein'
> 2 steps, 40.0 ps.
> step  200: timed with pme grid 64 80 60, coulomb cutoff 1.000: 3340.0
> M-cycles
> step  400: timed with pme grid 60 72 56, coulomb cutoff 1.075: 3742.2
> M-cycles
> step  600: timed with pme grid 60 80 56, coulomb cutoff 1.062: 3725.5
> M-cycles
> step  800: timed with pme grid 60 80 60, coulomb cutoff 1.037: 3667.2
> M-cycles
> step 1000: timed with pme grid 64 80 60, coulomb cutoff 1.000: 3564.0
> M-cycles
>   optimal pme grid 64 80 60, coulomb cutoff 1.000
> step 9400, remaining wall clock time:   104 s
>
>
>
> The last line is updated and the new line replaces the previous (last)
> line. I wonder why the first 100 steps are shown in separate lines ("\n").
> That is not happening with "-nb cpu".
>
>
>
> Any thought?
>
> Regards,
> Mahmood
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Re: [gmx-users] rerun from random seeds

[Szilárd Páll]

Yes, this will generate velocities with a random seed.
--
Szilárd


On Thu, Jul 5, 2018 at 5:15 PM MD  wrote:

> Hi Gromacs folks,
>
> I am trying to re-run a 100 ns simulation with different velocities and
> random seed. Would the setup from the mdp file as the following a good one?
>
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> Thanks in advance,
>
> Ming
> --
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[gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,

I am trying to perform a NVT equilibration. However, I obtain this error:

Fatal error:
Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

I don't understand the problem because I don't have defined any group,  I am 
indicating the ref-t and tau-t for the whole system.

My .mdp file is:

define  = -DPOSRES  ; position restrain the lipid

; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs

; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps

; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.2   ; short-range electrostatic cutoff (in 
nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in 
nm)

; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT

; Temperature coupling is on
tcoupl  = nose-hoover  ; nose-hoover thermostat
tau_t   = 0.1; time constant, in ps
ref_t   = 298; 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

; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme

; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 298   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


Could anyone help me?

Thank you in advance,
C.

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Re: [gmx-users] Making group of different atoms

[Chetan Puri]

Yes, I have tried but I am having trouble in making a group for atoms with
different numbers.

On Wed, 11 Jul 2018, 22:29 Quyen V. Vu,  wrote:

> Have you try make_ndx tool of Gromacs?
>
> On Wed, Jul 11, 2018, 00:09 Chetan Puri  wrote:
>
> > Can someone guide me in how to make a group for atoms number 1566, 1567,
> > 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of
> > protein.
> >
> > Since I need to measure distance between two groups (ligand and protein)
> >
> >
> > Regards,
> > Chetan
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Re: [gmx-users] Making group of different atoms

[Shrinath Kumar]

In the index editor of make_ndx does "a 1566 1567 1569 1571 1574 1579" not
work? Alternatively, you can just manually make the index file as Sohaib
suggested. An index group is just:

[ name_of_group ]
;atomnr of atoms that make up the group eg.
1566 1567 1569 1571 1574 1579 etc..

On 12 July 2018 at 16:24, Chetan Puri  wrote:

> Yes, I have tried but I am having trouble in making a group for atoms with
> different numbers.
>
> On Wed, 11 Jul 2018, 22:29 Quyen V. Vu,  wrote:
>
> > Have you try make_ndx tool of Gromacs?
> >
> > On Wed, Jul 11, 2018, 00:09 Chetan Puri  wrote:
> >
> > > Can someone guide me in how to make a group for atoms number 1566,
> 1567,
> > > 1569,1571,1574&1579, which all belong to a tyrosine residue number 128
> of
> > > protein.
> > >
> > > Since I need to measure distance between two groups (ligand and
> protein)
> > >
> > >
> > > Regards,
> > > Chetan
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
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Re: [gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

[Mark Abraham]

Hi,

You need to specify a group, eg System. That this is not the default
behavior protects you from making a typo and accidentally coupling the
whole system when it was not your intent.

Mark

On Thu, Jul 12, 2018, 17:24 Gonzalez Fernandez, Cristina <
cristina.gonzalezf...@unican.es> wrote:

> Dear Gromacs users,
>
> I am trying to perform a NVT equilibration. However, I obtain this error:
>
> Fatal error:
> Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values
>
> I don't understand the problem because I don't have defined any group,  I
> am indicating the ref-t and tau-t for the whole system.
>
> My .mdp file is:
>
> define  = -DPOSRES  ; position restrain the lipid
>
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 500   ; save coordinates every 1.0 ps
> nstvout = 500   ; save velocities every 1.0 ps
> nstenergy   = 500   ; save energies every 1.0 ps
> nstlog  = 500   ; update log file every 1.0 ps
>
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
>
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10; 20 fs, largely irrelevant with
> Verlet
> rcoulomb= 1.2   ; short-range electrostatic cutoff
> (in nm)
> rvdw= 1.2   ; short-range van der Waals cutoff
> (in nm)
>
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl  = nose-hoover  ; nose-hoover thermostat
> tau_t   = 0.1; time constant, in ps
> ref_t   = 298; 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
>
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell
> distribution
> gen_temp= 298   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
>
> Could anyone help me?
>
> Thank you in advance,
> C.
>
> --
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