Re: [gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences

[Justin Lemkul]

On 3/12/16 6:55 PM, fulvio ciriaco wrote:

Hello,
I have to simulate some non natural sequences containing sometimes both
T and U nucleic acids.
However pdb2gmx incorrectly detects the terminus, i.e., for a sequence like
TCAUA
it says
Identified residue DT1 as a starting terminus.
Warning: Residue RU4 in chain has different type (RNA) from starting residue DT1
(DNA).
Warning: Residue DA5 in chain has different type (DNA) from starting residue DT1
(DNA).
Identified residue DA3 as a ending terminus.

Then it does not treat DA5 as a ending terminus, i.e. , with amber99sb-ildn ff
Fatal error:
Atom H3T in residue DA 5 was not found in rtp entry DA with 32 atoms
while sorting atoms.

Is there some way to circumvent the excessive knowledge pdb2gmx has of 
biological
systems?



Make a local copy of residuetypes.dat and set RU to DNA.  pdb2gmx functions to 
prevent people from mixing things that shouldn't be mixed; if you are doing 
something strange, this is the only way to convince pdb2gmx to listen to you 
rather than its programming :)



I attach the tertiary structure for one such sequence.



The mailing list does not accept attachments, but none is necessary here.

-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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Re: [gmx-users] zero free energy of ligand in water

[Justin Lemkul]

On 3/12/16 3:43 AM, Sana Saeed wrote:

hi i have performed simple ligand only simulation (part of protein ligand
binding free energy calcultaion: alchemical pathway: from complex protein and
ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result
i got by using alchemical_analysis.py --> David Mobley's) but the only ligand
simulation (ligand+water) i am getting zeros for all lambda states. is it
fine? tahnks in advance


No, that makes no sense.  There should always be some amount of change in the 
free energy during the transformation.


-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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Re: [gmx-users] problem in editing .eps file of hbond

[Justin Lemkul]

On 3/12/16 5:44 AM, tasneem kausar wrote:

Dear all

I have plotted the hydrogen bonds present at the interface of protein in
its binary complex. I have already written the index file for the interface
residues then used it for hydrogen bond calculation. There are a number of
bonds at the interface. I am trying to put a cut off of 50 % for existence
of hydrogen bonds in the whole trajectroy. So I want to remove the rest of
hydrogen bonds of interface residues whose existence is less than 50% . For
this purpose how should I edit the .eps file. Because there are a lot of
data written and I am not able to understand the data that are given for x
and y axis.
Please solve the Issue


An .eps file is an image; I wouldn't advise trying to mess with its contents to 
get the information you want.  Everything you need should already be in the 
normal text output from hbond, most directly the hbmap.xpm file itself.  Parse 
that information to get what you want.


-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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Re: [gmx-users] Addendum to Question

[Justin Lemkul]

On 3/12/16 11:51 AM, Robert Molt wrote:

Thank you for clarifying the proper way to search the forums.

I was perhaps unclear in what I wrote. I already *have *the converted topology
and trajectory files (via Parmed). Rather, I am seeking the correct command to
combine them into a binary (pursuant to the use of do_x3dna
http://rjdkmr.github.io/do_x3dna/usage.html; this states I need to use a 
binary).

Am I incorrect in thinking I need to apply some form of the gmx command to a gro
trajectory file and a topology file to make a tpr file (which is a binary and
thus not directly convertible from what I have)?



You need to use grompp.  It creates a .tpr by combining coordinates (not 
trajectory!), topology, and simulation instructions (which in this case are 
arbitrary, as you only care to do analysis) into a binary input file with a .tpr 
extension.


-Justin


I will begin examining your tutorials, Dr. Lemkul. Thank you.



--
==

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] Addendum to Question

[Robert Molt]

Thank you for clarifying the proper way to search the forums.

I was perhaps unclear in what I wrote. I already *have *the converted 
topology and trajectory files (via Parmed). Rather, I am seeking the 
correct command to combine them into a binary (pursuant to the use of 
do_x3dna http://rjdkmr.github.io/do_x3dna/usage.html; this states I need 
to use a binary).


Am I incorrect in thinking I need to apply some form of the gmx command 
to a gro trajectory file and a topology file to make a tpr file (which 
is a binary and thus not directly convertible from what I have)?


I will begin examining your tutorials, Dr. Lemkul. Thank you.

--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

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Re: [gmx-users] Building Gromacs 5.1.2

[Mark Abraham]

Hi,

If you haven't installed it, then it isn't installed. Otherwise, you're not
running on the machine you think that you're running on...

Mark

On Sat, Mar 12, 2016 at 3:46 PM Okoroafor, Kelechi <
kelechi.okoroa...@gmail.com> wrote:

> Thank you very much, Mark, I greatly appreciate your assistance.
>
> I have Ubuntu 14.0.4 live booting from an external hard drive.
>
> And if I remember correctly, before correctly completing the installation,
> I had tried unsuccessfully to run “mdrun” and the command was not
> recognized.
> So I highly doubt that the distribution had Gromacs preinstalled.
>
> I shall go ahead and uninstall the currently installed version of Gromacs
> and try reinstalling version 5.1.2.
>
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Re: [gmx-users] Building Gromacs 5.1.2

[Okoroafor, Kelechi]

Thank you very much, Mark, I greatly appreciate your assistance.

I have Ubuntu 14.0.4 live booting from an external hard drive.

And if I remember correctly, before correctly completing the installation, I 
had tried unsuccessfully to run “mdrun” and the command was not recognized.
So I highly doubt that the distribution had Gromacs preinstalled.

I shall go ahead and uninstall the currently installed version of Gromacs and 
try reinstalling version 5.1.2.

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Re: [gmx-users] Building Gromacs 5.1.2

[Mark Abraham]

Hi,

That just means what it says. Be aware that some distributions provide
GROMACS packages, which it sounds like you might have.

Mark

On Sat, Mar 12, 2016 at 1:28 PM Okoroafor, Kelechi <
kelechi.okoroa...@gmail.com> wrote:

> Hello,
>
> I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted
> Linux system, which did not have Gromacs previously installed.
>
> When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with
> gpu disabled.
>
> Please has this happened to anyone else?
>
> Would any one know what I might have done wrong in the course of building
> and installing the software?
> --
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> posting!
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Re: [gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

[shrikant kaushik]

Thank you!

SHRI KANT
M Tech (Computational Biology)
Centre for Biotechnology
Anna University, Chennai
600025

On Fri, Mar 11, 2016 at 6:24 PM, Justin Lemkul  wrote:

>
>
> On 3/11/16 2:50 AM, shrikant kaushik wrote:
>
>> Dear all gromacs users,
>>[shrikant@Ares Simulation]$ gmx-5.1.2
>> mdrun -v -deffnm em
>> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>
>>  GROMACS is written by:
>>   Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>   Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
>> Fritsch
>>Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
>> Hindriksen
>>   Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
>> Kutzner
>>  Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>> Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons
>> Sijbers
>> Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>> and the project leaders:
>>  Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:  gmx mdrun, VERSION 5.1.2
>> Executable:   /usr/local/gromacs-5.1.2/bin/gmx-5.1.2
>> Data prefix:  /usr/local/gromacs-5.1.2
>> Command line:
>>gmx-5.1.2 mdrun -v -deffnm em
>>
>>
>> Running on 1 node with total 4 cores, 4 logical cores
>> Hardware detected:
>>CPU info:
>>  Vendor: GenuineIntel
>>  Brand:  Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
>>  SIMD instructions most likely to fit this hardware: AVX_256
>>  SIMD instructions selected at GROMACS compile time: AVX_256
>>
>> Reading file em.tpr, VERSION 5.1.2 (single precision)
>> Using 1 MPI thread
>> Using 4 OpenMP threads
>>
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.0e+03
>> Number of steps=5
>> Step=0, Dmax= 1.0e-02 nm, Epot=  1.64486e+07 Fmax= 3.27208e+07, atom=
>> 4176
>> Step=1, Dmax= 1.0e-02 nm, Epot=  1.55865e+07 Fmax= 3.13386e+07, atom=
>> 4176
>> Step=2, Dmax= 1.2e-02 nm, Epot=  1.46513e+07 Fmax= 2.97319e+07, atom=
>> 4176
>> Step=3, Dmax= 1.4e-02 nm, Epot=  1.36016e+07 Fmax= 2.78772e+07, atom=
>> 4176
>> Step=4, Dmax= 1.7e-02 nm, Epot=  1.24230e+07 Fmax= 2.57543e+07, atom=
>> 4176
>> Step=5, Dmax= 2.1e-02 nm, Epot=  1.3e+07 Fmax= 2.33503e+07, atom=
>> 4176
>> Step=6, Dmax= 2.5e-02 nm, Epot=  9.67180e+06 Fmax= 2.06643e+07, atom=
>> 4176
>> Step=7, Dmax= 3.0e-02 nm, Epot=  8.12309e+06 Fmax= 1.77136e+07, atom=
>> 4176
>> Step=8, Dmax= 3.6e-02 nm, Epot=  6.50058e+06 Fmax= 1.45408e+07, atom=
>> 4176
>> Step=9, Dmax= 4.3e-02 nm, Epot=  4.86276e+06 Fmax= 1.12217e+07, atom=
>> 4176
>> Step=   10, Dmax= 5.2e-02 nm, Epot=  3.30460e+06 Fmax= 7.87434e+06, atom=
>> 4176
>> Step=   11, Dmax= 6.2e-02 nm, Epot=  2.04717e+06 Fmax= 9.25255e+06, atom=
>> 75560
>> Wrote pdb files with previous and current coordinates
>>
>> ---
>> Program gmx mdrun, VERSION 5.1.2
>> Source code file:
>> /usr/local/src/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555
>>
>> Fatal error:
>>
>> step 12: Water molecule starting at atom 13529 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> Since it's EM that's failing, the most likely problem is unreasonable
> coordinates (mdrun is printing out likely locations of these nasty
> interactions!).  Since you've provided no other useful information about
> what you're doing or what your system is, that's the best advice that can
> be given.
>
> -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
> 

[gmx-users] Building Gromacs 5.1.2

[Okoroafor, Kelechi]

Hello,

I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux 
system, which did not have Gromacs previously installed.

When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu 
disabled.

Please has this happened to anyone else?

Would any one know what I might have done wrong in the course of building and 
installing the software?
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[gmx-users] Building Gromacs 5.1.2

[Okoroafor, Kelechi]

Hello,

I attempted installing Gromacs 5.1.2 with gpu enabled on a live booted Linux 
system, which did not have Gromacs previously installed.

When I ran “mdrun -version” I saw that Gromacs 4.6.5 was installed with gpu 
disabled.

Please has this happened to anyone else?

Would any one know what I might have done wrong in the course of building and 
installing the software?
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[gmx-users] problem in editing .eps file of hbond

[tasneem kausar]

Dear all

I have plotted the hydrogen bonds present at the interface of protein in
its binary complex. I have already written the index file for the interface
residues then used it for hydrogen bond calculation. There are a number of
bonds at the interface. I am trying to put a cut off of 50 % for existence
of hydrogen bonds in the whole trajectroy. So I want to remove the rest of
hydrogen bonds of interface residues whose existence is less than 50% . For
this purpose how should I edit the .eps file. Because there are a lot of
data written and I am not able to understand the data that are given for x
and y axis.
Please solve the Issue

Thanks in advance
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Re: [gmx-users] Optimal hardware for running Gromacs

[Kutzner, Carsten]

Dear David,

I think you will find answers to many of your questions in the following
publication:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full

Best,
  Carsten



> On 12 Mar 2016, at 02:52, David Berquist  wrote:
> 
> I'm looking into building a desktop computer for running Gromacs
> simulations.  I'd like to know how I should configure it to get the best
> performance possible for the price.
> 
> One example of something I might run on this system would be: simulate an
> ionic polymer of approximately 100k atoms for 1 millisecond.  Coarse
> grained atoms, using Martini force field.
> 
> I would be planning to spend something under $1500 on this system.
> 
> 
> 
> In regards to the graphics card, what factors are important?  I assume that
> the single precision Flop/s are a big factor, but what about memory
> bandwidth(on the card itself)?
> 
> I've noticed that Gromacs pages on GPUs tend to recommend nVidia cards,
> specifically those with CUDA Compute Capability 5.2.  But, AMD Radeon cards
> appear to offer the same processing power for far lower prices(or
> alternatively, significantly more processing power for the same price).
> 
> For example, the nVidia GTX 970 offers 3494 GFlop/s of single precision,
> and 109 GFlop/s of double precision.  It currently costs $290 at Newegg.
> On the other hand, the AMD Radeon R9 380 provides 3476.5 GFlop/s single
> precision, and 217.3 GFlop/s of double precision.  It currently costs $150
> on Newegg.
> 
> That's practically the same single precision, and nearly double the
> double-precision for around half the price.
> 
> Or, for about the same price as the nVidia GTX 970 I could get an AMD
> Radeon R9 390.  It provides 5120 GFlop/s of single precision and 640
> GFlop/s of double precision.  That costs $310 on Newegg.
> 
> That is, on paper, 46.5% more single precision performance, and 487% more
> double precision performance(nearly 5 times as much) for only a 6.9% higher
> price.
> 
> So, does Gromacs run a lot faster on nVidia GPUs?  Would the nVidia GTX 970
> provide similar or better performance than the AMD Radeon R9 390?
> 
> One more GPU Question; does Gromacs scale linearly across multiple graphics
> cards?   So, if I have two identical cards which offer 2000 GFlop/s
> performance each, would they both together perform about the same as a
> more-expensive single card which provides 4000GFlop/s(provided you have a
> fast enough CPU, of course)?
> 
> 
> 
> Now, how about the CPU performance?  Would it be better to spend a lot of
> my budget on a high-end GPU, and then go for a low cost CPU?  Something
> like an  AMD Athlon X4 860K Kaveri Quad-Core 3.7 GHz CPU?  Or would
> something like that bottleneck the performance of an nVidia GTX 970 or GTX
> 980?  Maybe a AMD FX-6300 Vishera 6-Core 3.5 GHz?  AMD FX-8300 Vishera
> 8-Core 3.3GHz?
> Does Intel vs AMD make any significant difference?  When running Gromacs on
> a system with GPU compute turned on, what sort of computing load does
> Gromacs put on the CPU?  Is there any commonly used CPU benchmark that can
> be used to approximate relative Gromacs performance between CPUs?
> 
> 
> 
> How important is the system RAM speed?  Should I spend more of my budget
> building a DDR4 system(more expensive CPU, motherboard, and RAM modules),
> or would that not make a significant difference over DDR3?
> 
> Would you happen to know what quantity of memory should be sufficient for
> common Gromacs simulation runs, or runs such as the example I included
> above?
> 
> 
> Finally, does the speed of the hard drive impact Gromacs performance?  The
> options are a cheap spinning-platter hard drive(100-200MB/s sequential
> write), a low-cost SSD(400-500MB/s sequential write), or a high-speed PCI-E
> SSD(1000-1500MB/s sequential write).  Would writing out the data(.xtc,
> .trr, .edr) to a slower hard drive(100-200MB/s sequential write speed)
> cause the Gromacs simulation to slow down?
> I don't see any reason that a cheap spinning platter hard drive would slow
> Gromacs simulations down, but I want to make sure I'm not missing
> anything.
> 
> Thank you for your time.  I'd be very grateful for any information you can
> give me, or direct me to.
> 
> David Berquist
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[gmx-users] zero free energy of ligand in water

[Sana Saeed]

hi i have performed simple ligand only simulation (part of protein ligand 
binding free energy calcultaion: alchemical pathway: from complex protein and 
ligand simulation i got 11.43 kj/mol of delta G by using gmx bar, same result i 
got by using alchemical_analysis.py --> David Mobley's) but the only ligand 
simulation (ligand+water) i am getting zeros for all lambda states. is it fine? 
tahnks in advance  Sana Saeed Khan,Research AssistantChemoinformatics 
LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, 
Seoul, South Korea.
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