Re: [gmx-users] help required in calculating npme value for domain decomposition

[Sarath Chandra]

Please refer to documentation on tune_pme in version 5.1.2 or g_tune_pme in
older versions of gromacs.

Regards,

Sarath


On 19 May 2016 at 23:43, Antara mazumdar  wrote:

> Dear gromacs users,
>
>   I need help in calculating the value of npme for the purpose of domain
> decomposition for my system of mixed lipid vesicles.
>
>
> Thanks!!
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
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Re: [gmx-users] simulation_time[Nikita Bora]

[Ms. Nikita Bora]

Thanks Tsjerk

That was really a good explanation. And it helped me out a lot.
Still,I would like to know what are the standard values for these
parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.

As earlier it was mentioned that with different force field different
value is used so is there any link where i can get to know the minimum cut
off values for these parameters and which value should be used for which
force field or condition

thanks
Nikita



  Original Message 
> Subject: Re: simulation_time
> From:"Ms. Nikita Bora" 
> Date:Mon, May 16, 2016 9:42 am
> To:  nik...@tezu.ernet.in
> --
>
> Respected Sir,
>
> Thanks for the reply. I would further like to know that according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> the rvdw=rcoulomb=1 is used for the protein while according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> and protein-ligand complex is used??
>

Different force fields, different settings.

-Justin

>


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[gmx-users] help required in calculating npme value for domain decomposition

[Antara mazumdar]

Dear gromacs users,

  I need help in calculating the value of npme for the purpose of domain
decomposition for my system of mixed lipid vesicles.


Thanks!!
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Antara mazumdar]

Dear users,

Is there any script available to calculate % occupancy of residues with
respect to time? This in continuation with my previous query on percentage
of protein in contact with membrane??

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Thu, May 19, 2016 at 6:35 PM, Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I have a peripheral membrane protein which I have simulated using Charmm
> 36 in a mixed lipids bilayer. I want to calculate the percentage of protein
> in contact with membrane wrt time. I already have residue wise distances
> from membrane calculated.
>
> Can anyone suggest me how to go about it after this?
>
> Antara Mazumdar
>
> ISCB SC RSG-India
>
> Core Committee Member
>
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Re: [gmx-users] Pull code slows down mdrun -- is this expected?

[Christopher Neale]

Dear Szilárd:

I think that my ranks were set up similarly for GPU and non-GPU runs, though 
you can see how I ran the jobs below. One thing that I also already checked, 
but that I have not pasted here, is that all runs got the same DD and PME grid 
reported from the log file (4x1x1 for each in all cases), and that the 
nstlist/rlist modification was always the same (promoted to nstlist=40 / 
rlist=1.253)

Below I provide the run command and the end of the log files for:

(1) no pull-code with GPUs -- v5.1.2

(2) 1 pull-code cylinder restraint with GPUs -- v5.1.2

(3) 128 pull-code cylinder restraints with GPUs -- v5.1.2

(4) no pull-code with CPUs -- v5.1.2

(5) 1 pull-code cylinder restraint with CPUs -- v5.1.2

(6) 128 pull-code cylinder restraints with CPUs -- v5.1.2

(7) 128 pull-code cylinder restraints with CPUs -- Gromacs-2016-beta1


(1) no pull-code with GPUs

/home/cneale/exec/GROMACS/exec/gromacs-5.1.2/gpu_serial/bin/gmx mdrun 
-notunepme -deffnm MD -dlb yes -npme 0 -cpt 60 -maxh 0.01 -cpi MD.cpt -ntmpi 4 
-ntomp 6 -gpu_id 0123

M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V=Potential and force  V=Potential only  F=Force only

 Computing:   M-Number M-Flops  % Flops
-
 NB VdW [V]   364.832000 364.832 0.0
 Pair Search distance check1620.797488   14587.177 0.0
 NxN Ewald Elec. + LJ [F]483561.29164837717780.74995.2
 NxN Ewald Elec. + LJ [V]4927.352384  635628.458 1.6
 1,4 nonbonded interactions 509.305472   45837.492 0.1
 Calc Weights  1226.587986   44157.167 0.1
 Spread Q Bspline 26167.210368   52334.421 0.1
 Gather F Bspline 26167.210368  157003.262 0.4
 3D-FFT   87418.239194  699345.914 1.8
 Solve PME   30.8283041973.011 0.0
 Reset In Box10.256532  30.770 0.0
 CG-CoM  10.292394  30.877 0.0
 Bonds   71.5070724218.917 0.0
 Propers631.889024  144702.586 0.4
 Impropers2.918656 607.080 0.0
 Virial  41.123922 740.231 0.0
 Update 408.862662   12674.743 0.0
 Stop-CM  4.159992  41.600 0.0
 Calc-Ekin   81.8370842209.601 0.0
 Lincs  249.823000   14989.380 0.0
 Lincs-Mat 2355.1099849420.440 0.0
 Constraint-V   961.2418697689.935 0.0
 Constraint-Vir  35.598117 854.355 0.0
 Settle 153.879318   49703.020 0.1
-
 Total39616926.018   100.0
-


D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 28471.3
 av. #atoms communicated per step for LINCS:  2 x 2103.2

 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load imbalance: 0.2 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 %


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 4 MPI ranks, each using 6 OpenMP threads

 Computing:  Num   Num  CallWall time Giga-Cycles
 Ranks Threads  Count  (s) total sum%
-
 Domain decomp. 46286   1.093 62.827   3.0
 DD comm. load  46285   0.002  0.123   0.0
 DD comm. bounds46286   0.004  0.251   0.0
 Neighbor search46286   0.581 33.383   1.6
 Launch GPU ops.46  22802   0.962 55.297   2.7
 Comm. coord.   46  5   0.839 48.251   2.3
 Force  46  11401  11.241646.160  31.3
 Wait + Comm. F 46  11401   0.803 46.166   2.2
 PME mesh   46  11401  12.488717.838  34.8
 Wait GPU nonlocal  

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Tsjerk Wassenaar]

Hi Antara,

You can also simply calculate the ratio of buried surface area to total
surface area, which you can both get with gmx sasa

Cheers,

Tsjerk

On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:

> You can use g_contacts tool which will give you list of residues which are
> in contact with the membrane and their frequencies. You might have to write
> an overhead script to convert the residues in contact to %Protein in
> contact
>
> http://www.sciencedirect.com/science/article/pii/S0010465513002464
>
> Regards,
>
> Sarath
>
> --
> Sarath Chandra Dantu, PhD, ELS
> Room No. 606, New BSBE Building
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> Powai Mumbai, 400-076, India
>
>
> On 19 May 2016 at 18:35, Antara mazumdar  wrote:
>
> > Dear gromacs users,
> >
> > I have a peripheral membrane protein which I have simulated using Charmm
> 36
> > in a mixed lipids bilayer. I want to calculate the percentage of protein
> in
> > contact with membrane wrt time. I already have residue wise distances
> from
> > membrane calculated.
> >
> > Can anyone suggest me how to go about it after this?
> >
> > Antara Mazumdar
> >
> > ISCB SC RSG-India
> >
> > Core Committee Member
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS.

[André Farias de Moura]

Hi Barret,

authors of that paper state which units they are using for energy, distance
and angles - all other units might be inferred from units reasoning. For
your specific concern, kb must have units of eV/Ų in their tables of
parameters, leading to kJ/mol/nm² in the GROMACS convention after proper
conversions are applied.

If you're not 100% sure about that, you may either contact the authors of
that paper or check the original references from where they have taken
these parameters.

best,

Andre

On Wed, May 18, 2016 at 6:45 PM, Barrett Worley  wrote:

> Thanks for your reply, Andre.
>
> I get that I need to convert units. According to the GROMACS manual, kb
> units are kJ/mol*nm^2. However, the paper lists K in eV and the
> equation for harmonic bonds and angles: K×(r-r0)^2, which would give me
> eV*Å^2 (which I then convert Å to nm). These two sets of units are
> incommensurate, yes?
>
>
>
> On Wed, May 18, 2016 at 4:29 PM, André Farias de Moura 
> wrote:
>
> > Hi Barret,
> >
> > It looks like you just have to make the proper conversion of units (eV to
> > kJ/mol and angstrom to nm), but Lennard-Jones seems to be a little
> tricky,
> > since the authors defined different S-S interactions for atom in the same
> > plane or in different planes (not an issue if you are planning
> single-sheet
> > models).
> >
> > best
> >
> > Andre
> >
> > On Wed, May 18, 2016 at 6:12 PM, Barrett Worley 
> > wrote:
> >
> > > Hello all,
> > >
> > > I'm trying to modify the OPLS-AA force field parameters for Mo and S
> > atoms
> > > to simulate monolayer MoS2. I'm following the general procedure
> suggested
> > > here: http://chembytes.wikidot.com/grocnt
> > > <
> > >
> >
> http://www.linkedin.com/redir/redirect?url=http%3A%2F%2Fchembytes%2Ewikidot%2Ecom%2Fgrocnt=VkOA&_t=tracking_anet
> > > >,
> > > but they use existing OPLS-AA values for atomtypes, bondtypes, etc. To
> my
> > > knowledge, there is no Mo atom in OPLS-AA standard force fields.
> > >
> > > I've read the Varshney paper "MD simulations of molybdenum disulphide
> > > (MoS2): Force-field parameterization and thermal transport behavior,"
> and
> > > would like to use the parameters listed there in my force field.
> However,
> > > I'm having difficulty translating their parameters for set 9 into
> > relevant
> > > GROMACS .itp parameters.
> > >
> > > For example, how would one translate bond coefficients K and r0 to
> > > bondtypes values b0 and kb? Or am I even on the right track?
> > >
> > > Any help on this matter would be greatly appreciated!
> > >
> > > Thanks,
> > >
> > > Barrett
> > >
> > > --
> > > Barrett Worley
> > > Doctoral Candidate
> > > Dodabalapur Group
> > > Dept. of Chemistry
> > > The University of Texas at Austin
> > > --
> > > 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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > _
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
> > Gromacs Users mailing list
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> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> Barrett Worley
> Doctoral Candidate
> Dodabalapur Group
> Dept. of Chemistry
> The University of Texas at Austin
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>



-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] Generating topology for a hem protein

[Justin Lemkul]

On 5/19/16 9:41 AM, zeineb SI CHAIB wrote:


Dear all,

I'm desperetly looking for help to generate the topology of my hem protein.


   I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals
that should not exist and it's complicated to verify everything. Justin
suggested using CHARMM-GUI, I followed a tutorial that I found on line
(http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build
my system, I'm in the final step, adding the Hem group to my protein but I
don't know how to do it and I don't know if all the steps went well or not.



If you don't know, how can anyone on this list know?  If something went wrong 
with CHARMM-GUI, there would be a fatal error.  It's as simple as uploading the 
PDB file and letting CHARMM-GUI do the work; our latest version even writes all 
the GROMACS topologies and input files for you.  It will generate the correct 
dihedrals for heme groups.


Unless you can provide a specific issue (with GROMACS, because this is not the 
place for CHARMM-GUI problems), there's nothing anyone can do to help you.  We 
can't guess what the problem is, and in this instance, you haven't even said if 
there is a problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Generating topology for a hem protein

[zeineb SI CHAIB]

Dear all, 

I'm desperetly looking for help to generate the topology of my hem protein. 





I'm using CHARMM as a force field and apparently PDB2gmx assigns 
dihedrals that should not exist and it's complicated to verify everything. 
Justin suggested using CHARMM-GUI, I followed a tutorial that I found on line 
(http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build my 
system, I'm in the final step, adding the Hem group to my protein but I don't 
know how to do it and I don't know if all the steps went well or not. 

Any advices, HELP please!! I'll really appreciate your help, time and patience! 

Regards. 

Zeinbe. 



  
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Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Sarath Chandra]

You can use g_contacts tool which will give you list of residues which are
in contact with the membrane and their frequencies. You might have to write
an overhead script to convert the residues in contact to %Protein in contact

http://www.sciencedirect.com/science/article/pii/S0010465513002464

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 19 May 2016 at 18:35, Antara mazumdar  wrote:

> Dear gromacs users,
>
> I have a peripheral membrane protein which I have simulated using Charmm 36
> in a mixed lipids bilayer. I want to calculate the percentage of protein in
> contact with membrane wrt time. I already have residue wise distances from
> membrane calculated.
>
> Can anyone suggest me how to go about it after this?
>
> Antara Mazumdar
>
> ISCB SC RSG-India
>
> Core Committee Member
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Help required for calculation of protein coverage % wrt time

[Antara mazumdar]

Dear gromacs users,

I have a peripheral membrane protein which I have simulated using Charmm 36
in a mixed lipids bilayer. I want to calculate the percentage of protein in
contact with membrane wrt time. I already have residue wise distances from
membrane calculated.

Can anyone suggest me how to go about it after this?

Antara Mazumdar

ISCB SC RSG-India

Core Committee Member
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Re: [gmx-users] Gromacs installation.

[Elsaid Younes]

 http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz
I think that something makes this link not downloadable. When I disable the
download from -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON by
deleting -DREGRESSIONTEST_DOWNLOAD=ON asking me to
make GMX_BUILD_UNITTESTS=ON
Then after I made it, I still get this
Total Test time (real) = 165.57 sec
[100%] Built target run-ctest
[100%] Unit tests disabled
NOTE: Unit tests have not been run. You need to set GMX_BUILD_UNITTESTS=ON
if you want to build and run them.
[100%] Built target unittests-notice
[100%] Built target check..After all Gromacs can not start.



On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes  wrote:

> Hi all,
>
> I have installed gromacs like the quick and dirty installation. I have a
> 16.04 version of ubuntu. I can not start it.
> I used to do the same procedure in ubuntu 15.10, and it worked fine.
>
> /Elsaid
>
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