date:20140911

Re: [gmx-users] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Carsten Kutzner


On 11 Sep 2014, at 05:03, Johnny Lu johnny.lu...@gmail.com wrote:

 Does writing frequently (like position, velocity, energy, log every 10
 timesteps) significantly slow down the simulation?
Probably yes, have a look at the md.log output file
and how much percent is spent in write traj.

Carsten


 
 On Wed, Sep 10, 2014 at 10:31 PM, Johnny Lu johnny.lu...@gmail.com wrote:
 
 tried that, and the result was:
 
 Reading file npt.tpr, VERSION 5.0.1 (double precision)
 Changing nstlist from 10 to 40, rlist from 1 to 1.028
 
 The number of OpenMP threads was set by environment variable
 OMP_NUM_THREADS to 48
 Using 1 MPI thread
 Using 48 OpenMP threads
 
 WARNING: Oversubscribing the available 24 logical CPU cores with 48
 threads.
 This will cause considerable performance loss!
 
 ---
 Program mdrun_d, VERSION 5.0.1
 Source code file:
 /export/data1/kho/software/gromacs5.1/gromacs-5.0.1/src/gromacs/mdlib/nbnxn_search.c,
 line: 2577
 
 Fatal error:
 48 OpenMP threads were requested. Since the non-bonded force buffer
 reduction is prohibitively slow with more than 32 threads, we do not allow
 this. Use 32 or less OpenMP threads.
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---
 
 so. i guess that is not a good idea.
 
 On Wed, Sep 10, 2014 at 9:55 PM, Johnny Lu johnny.lu...@gmail.com wrote:
 
 that 8-20% performance increase was for gromacs 4.6.5
 
 On Wed, Sep 10, 2014 at 9:52 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
 Is it a good idea to use 48 OpenMP thread, under 1 MPI thread on 24 Xeon
 Processors?
 
 The mail list say such practice give about 8-20% performance increase
 
 Should I try g_tune_pme when I searched for imbalance in the log file
 and found nothing (24 OMP thread under 1 MPI thread on 24 Xeon Processor)?
 Or is that done automatically?
 
 Does gromacs support double precision calculation on GPU if the hardware
 supports that?
 
 The optimize fft option is also obsolete.
 
 Thanks again.
 
 
 
 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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http://www.mpibpc.mpg.de/grubmueller/sppexa

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[gmx-users] Bond Energy question.

2014-09-11 Thread Dan Sponseller

Hello.

I have completed a simulation with two polyethylene glycol (PEG) molecules and 
then minimized the final conformation. As a demonstration that the two 
molecules wish to stick together, I separate the two molecules manually and run 
a single minimization step. I inspect the energy log file since it reports the 
energies at step zero. I show that the Potential energy is higher in the 
separated molecules which completes the demonstration.

However, I also notice that the G96Bond energy is almost double. Since the 
atoms within each molecule have not moved relative to each other at step zero, 
should not the bond energy not have changed? The G96Bond energy should just be 
reporting the interaction between bonded atoms, correct?

Thanks for any insight.

Dan Sponseller
PhD student
George Mason University
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[gmx-users] Principal axes of inertia and g_principal

2014-09-11 Thread nicola staffolani

Dear GMX community,

regarding the program g_principal and acknowledged the bug reported here
http://permalink.gmane.org/gmane.science.biology.gromacs.user/66719
, I would like to understand what the meaning of the output of this
program is.
So, left aside moi.dat, the output files are axis1.dat, axis2.dat 
axis3.dat.
Supposing that I have already corrected the output files (or reinstalled
GROMACS having fixed the bug in the source file as explained always here
http://t110399.science-biology-gromacs-user.biotalk.us/g-principal-bug-or-very-bad-choice-of-filenames-t110399.html),
in each of the files, for each time instant there are three coordinates: x,
y and z: what do they mean? My interpretation is that if I connect the
point, whose coordinates are those printed out in the output files, with
the origin of the Cartesian axes, then I get a line coinciding with the
corresponding (principal) axis: is this interpretation correct?

To get the principal axes, I have to diagonalize the moment of inertia
symmetric 3×3 matrix; one way to do it is by solving the 3rd order equation
for the eigenvalues: is this the way by which GROMACS finds then the
eigenvectors of the moment of inertia matrix, from which it calculates the
aforementioned coordinates?

Thank you in advance,

Nicola   

-- 
Nicola Staffolani PhD
Biophysics  Nanoscience Centre http://www.unitus.it/biophysics
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffol...@unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36
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Re: [gmx-users] itp file

2014-09-11 Thread Lalita Shaki

Hi Lovika,

You can't use the .itp file from GROMOS for other
forcefield. Which kind of molecule are you studying?
For generating the .itp file is usually use the pdb2gmx
tool.

Regards

Lalita


 Message: 1
 Date: Thu, 11 Sep 2014 10:22:39 +0530
 From: Lovika Moudgil lovikamoud...@gmail.com
 To: gmx-us...@gromacs.org gmx-us...@gromacs.org
 Subject: [gmx-users] itp file
 Message-ID:
 CANz=wd=
 ccwj65te2vc5ezf_3k_nos0yfxrkusx+bf1wzkgr...@mail.gmail.com
 Content-Type: text/plain; charset=UTF-8

 Hi everyone ,

 Need some help  . I am using OPLS/AA force field . I am generating .itp
 file from external tool , But these tools are using GROMOS force fields .
 Is it fine to use these .itp files with OPLS/AA force field ?? Or if its
 not fine to use these file with different force field than how can I
 generate .itp files for OPLS/AA ?


 Thanks and Regards
 Lovika



-- 
Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz
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Re: [gmx-users] itp file

2014-09-11 Thread Lovika Moudgil

Thanks for reply Lalit , Actually  my system have citrate anion and I want
.itp for citrate and further I will use OPLA/SS force field!! It can't be
generated be pdb2gmx!!

Regards
Lovika

On Thu, Sep 11, 2014 at 3:35 PM, Lalita Shaki lalitash...@gmail.com wrote:

 Hi Lovika,

 You can't use the .itp file from GROMOS for other
 forcefield. Which kind of molecule are you studying?
 For generating the .itp file is usually use the pdb2gmx
 tool.

 Regards

 Lalita


  Message: 1
  Date: Thu, 11 Sep 2014 10:22:39 +0530
  From: Lovika Moudgil lovikamoud...@gmail.com
  To: gmx-us...@gromacs.org gmx-us...@gromacs.org
  Subject: [gmx-users] itp file
  Message-ID:
  CANz=wd=
  ccwj65te2vc5ezf_3k_nos0yfxrkusx+bf1wzkgr...@mail.gmail.com
  Content-Type: text/plain; charset=UTF-8
 
  Hi everyone ,
 
  Need some help  . I am using OPLS/AA force field . I am generating .itp
  file from external tool , But these tools are using GROMOS force fields .
  Is it fine to use these .itp files with OPLS/AA force field ?? Or if its
  not fine to use these file with different force field than how can I
  generate .itp files for OPLS/AA ?
 
 
  Thanks and Regards
  Lovika
 
 

 --
 Lalita S. Uribe.
 European Master in Theoretical Chemistry and Computational Modeling.
 PhD student. Johannes Gutenberg-Universität Mainz
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[gmx-users] PBC problem in bilayer system

2014-09-11 Thread shahab shariati

Dear Gromacs users

Unfortunately, no one did not answer my previous question about
selection of appropriate option for trjconv -pbc to solve pbc problem.

For preparation of initial system, I inserted 4 drug molecules in
close vicinity to the membrane surface in water phase, in one side of
bilayer.

I obtained the Z coordinate (along the bilayer normal) of the center
of mass of the 4 drug molecules (violet, blue, red and green lines)
and DPPC lipid bilayer (black line) as a function of simulation time,
using g_traj tool.

The related figure is in following link:

https://www.dropbox.com/s/op8gaxeto4z7qxq/figure.TIF?dl=0

Do this state is related to pbc problem?

How to solve this issue?

Any help will highly appreciated.
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[gmx-users] Net charge density distribution plots in GROMACS

2014-09-11 Thread soumadwip ghosh

Hello,
  I am calculating Mg2+ concentration dependent persistence length
calculation of RNA strands. Since, the trends of RNA chain collapse is
different for different ionic concentration, I need to quantify if there is
overcharging at higher concentration of divalent cation. For this, I have
to show a charge density distribution against the distance of the RNA at
different salt concentration. I am using GROMACS 4.5.6 and could not find
this particular tool. Kindly help me as  its one of the reviews from the
referee.

Regards,
Soumadwip
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Re: [gmx-users] Net charge density distribution plots in GROMACS

2014-09-11 Thread João Henriques

Hello,

First of all don't be offended, but I struggled a little bit with your
English, so I hope I got the message correctly. If my answer doesn't
correspond to your question, please let me know.

 I am using GROMACS 4.5.6 and could not find this particular tool.

That's because there isn't one. Gromacs is a MD package, you are looking in
the wrong place. To calculate charge distributions you need a titration
scheme. A constant-pH MD method would probably be able to do so, but then
there are the Mg2+ cations. Divalent (multivalent) ions are usually a
problem, specially when using a linearized Poisson Boltzmann solver to
estimate the pKa's (this is part of the internal machinery used in
constant-pH MD methods).

There are other alternative methods.

Best regards,
João

On Thu, Sep 11, 2014 at 1:30 PM, soumadwip ghosh soumadwipgh...@gmail.com
wrote:

 Hello,
   I am calculating Mg2+ concentration dependent persistence length
 calculation of RNA strands. Since, the trends of RNA chain collapse is
 different for different ionic concentration, I need to quantify if there is
 overcharging at higher concentration of divalent cation. For this, I have
 to show a charge density distribution against the distance of the RNA at
 different salt concentration. I am using GROMACS 4.5.6 and could not find
 this particular tool. Kindly help me as  its one of the reviews from the
 referee.

 Regards,
 Soumadwip
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Re: [gmx-users] Contact angle measurement on a flat surface

2014-09-11 Thread Mark Abraham

Hi,

Petter Johanson here in Berk's group does some similar things in a fairly
ad-hoc way (bin the density profile), but he suggests the methods here
http://www.mdpi.com/1099-4300/15/9/3734 might be useful.

Mark


On Wed, Sep 10, 2014 at 5:45 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Dear all,

 I would like to know what are the methods I could use to measure/plot the
 contact angle of a water nanodroplet on flat graphene.

 Is there a script or tool in GROMACS that can perform the contact angle
 calculation?

 I am aware that the commonly used Young's equation does not apply here,
 since the droplet sizes will be in nanoscale.


 The modified Young-Dupre's equation, and other plotting methods such as
 the graphical binning approach by Werder et al. J. Phys. Chem. B 107,
 1345-1352 (2003),

 and the algorithm method by Ingebrigtsen and Toxvaerd, J. Phys. Chem. C
 111, 8518 (2007) provided some theory on the calculation,

 but I would like to know about the technical steps on doing the
 measurement.


 Any feedback is greatly appreciated.

 Thank you in advance.


 Regards,

 Kester


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Re: [gmx-users] Bond Energy question.

2014-09-11 Thread Mark Abraham

On Thu, Sep 11, 2014 at 9:24 AM, Dan Sponseller grom...@danpeg.com wrote:

 Hello.

 I have completed a simulation with two polyethylene glycol (PEG) molecules
 and then minimized the final conformation. As a demonstration that the two
 molecules wish to stick together, I separate the two molecules manually and
 run a single minimization step. I inspect the energy log file since it
 reports the energies at step zero. I show that the Potential energy is
 higher in the separated molecules which completes the demonstration.

 However, I also notice that the G96Bond energy is almost double. Since the
 atoms within each molecule have not moved relative to each other at step
 zero, should not the bond energy not have changed?


Not true. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy


 The G96Bond energy should just be reporting the interaction between bonded
 atoms, correct?


Yes

Mark


 Thanks for any insight.

 Dan Sponseller
 PhD student
 George Mason University
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Re: [gmx-users] itp file

2014-09-11 Thread Justin Lemkul




On 9/11/14 6:09 AM, Lovika Moudgil wrote:

Thanks for reply Lalit , Actually  my system have citrate anion and I want
.itp for citrate and further I will use OPLA/SS force field!! It can't be
generated be pdb2gmx!!



The OPLS-AA strategy is generally similar to GROMOS - you can piece the molecule 
together from existing functional groups.  Since the force field already covers 
everything you need for citrate, assigning charges and atomtypes is 
straightforward.  You can create an .rtp entry for it and have pdb2gmx do all 
the work of assigning the bonded interactions (you need to specify the [bonds], 
pdb2gmx does the rest).


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] PBC problem in bilayer system

2014-09-11 Thread Justin Lemkul




On 9/11/14 8:01 AM, shahab shariati wrote:

Dear gromacs users

When I see trajectory file using vmd, there is state showed in following link:

https://www.dropbox.com/s/g8i934atodrb7te/figure2.TIF?dl=0

in initial structure, all 4 drugs were  inserted in water phase, in one side of
bilayer.

Is this state normal?



Yes, because there's no such thing as a side in a periodic system.  You have a 
water layer that is continuous in z, so the molecules are free to diffuse around 
as they please.  It may not be possible to re-image the trajectory such that all 
of the drug molecules are positioned in the same region in the unit cell.  You 
can try the translation options of trjconv (in conjunction with -pbc mol) to try 
to shift the system up or down to get everything to fit, but then of course the 
lipids can jump around.  Perhaps additional calls to trjconv can account for 
that (i.e. another round of -pbc nojump after translating).


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Mark Abraham

Hi,

Hyper-threading is generally not useful with applications that are compute-
or network-bound, as GROMACS is. You should expect to see maximum
performance when using one real thread per x86 core (and you should find
out how many cores really exist, and not infer it from something else). You
should start with an MPI  rank per core (thus one thread per rank), and
consider reducing the number of ranks by having more OpenMP threads per
rank - but this is generally only useful for non-GPU runs when running on a
lot of Intel x86 hardware.

On Thu, Sep 11, 2014 at 3:52 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Is it a good idea to use 48 OpenMP thread, under 1 MPI thread on 24 Xeon
 Processors?


No.


 The mail list say such practice give about 8-20% performance increase


If it did, that might have been in context of managing the work done on the
CPU while using a GPU, which is not what you are doing. But without a link,
the reference is useless...

Should I try g_tune_pme when I searched for imbalance in the log file and
 found nothing (24 OMP thread under 1 MPI thread on 24 Xeon Processor)? Or
 is that done automatically?


You're not using more than one rank, so there's not really any load
imbalance to tune - it's just bad.

Does gromacs support double precision calculation on GPU if the hardware
 supports that?


No.


 The optimize fft option is also obsolete.


Yes, it got removed before 5.0, but there were a few things left in the
docs which I have now removed. Thanks.

Mark


 Thanks again.
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Re: [gmx-users] Constraint and Temperature Drop in NVE

2014-09-11 Thread Justin Lemkul




On 9/10/14 9:45 PM, Johnny Lu wrote:

Somehow I thought about mice, maze, cheese, and food poisoning.

What are the advantages of using multiple thermostat?



https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/075002.html

There are many other posts in the archive with more information.  It's not so 
much an advantage as it is a tactic to overcome problems in nonbonded schemes, 
which are greatly reduced when using PME.


-Justin


On Wed, Sep 10, 2014 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote:




On 9/10/14 4:29 PM, Mark Abraham wrote:


Hi,

On Wed, Sep 10, 2014 at 5:40 PM, Johnny Lu johnny.lu...@gmail.com
wrote:

  hmm. If that is the case, I have two questions.

1. Why gromacs doesn't adopt the method of measuring temperature as
described in the JCTC paper?
  (

https://www.deshawresearch.com/publications/Equipartition%20and%20the%
20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf
)



As they note in the discussion, this is not a practical approach for use
in
a *thermostat* because you need to estimate the time derivative of the
position. During the simulation you can only do a one-sided interpolation
from previous points, so using such an estimator makes the integration
scheme irreversible, which has its own drawbacks. So, an error exists in
the momentum-squared-based estimator of the temperature (from
finite-time-step size effects), and feeds back into the NVT integration
scheme. Whether this matters for the quality of the observables from a
given simulation is an open question, but their NVT results suggest that
time steps of the usual sizes are not good in combination with multiple
thermostats on small-ish systems. They used a Berendsen thermostat, which
is known to sample the wrong ensemble, so their NVT results may not be
quantitatively accurate, but offhand I'd expect to observe the trend they
see.

Naturally, one could write code to do two-sided interpolation as they do
there and so get a reliable temperature estimate in post-processing, but
nobody has bothered to do that. BTW, GROMACS does report the conserved
quantity for all integration schemes that have one.

Mark

2. As the paper mentioned that using two thermostats can cause hot solvent


cold solute problem for the timesteps that we commonly use, why do your
lysozyme tutorial still use two thermostats?
  (

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
gmx-tutorials/lysozyme/Files/nvt.mdp




To this point, the tutorials aim to provide simple, robust systems with
reproducible results that use common practices.  As I note fairly
prominently in all of my tutorials, no one should view the .mdp files as
definitively correct for anything you might want to do.  They work in their
intended context and that is the main point.  Multiple thermostats are
common practice, though recent literature has of course indicated that
different approaches may be better.  Strictly speaking, multiple
thermostats are a violation of equipartition of energy, but there were
practical reasons why they were used.

Perhaps it should also be said that tutorials linked from the Gromacs page
are provided as a convenience to users and are not intended as an
endorsement by the Gromacs developers.  The tutorials are the
responsibility of their individual authors.  Of course, I realize that in
my case, I am both... ;)

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Szilárd Páll

That many threads will most likely not be very efficient. If you are
running on a single node it could be the case that 1 rank with 24
OpenMP threads will still the the fastest configuration, but 48 will
be too much.
Depending on how imbalanced your system is using DD can still be
faster, so I suggest that you try I suggest that you also try a few
configurations, e.g 12 ranks 2/4 threads, 8 ranks 3/6 threads, etc.


On Thu, Sep 11, 2014 at 4:31 AM, Johnny Lu johnny.lu...@gmail.com wrote:
 tried that, and the result was:

 Reading file npt.tpr, VERSION 5.0.1 (double precision)
 Changing nstlist from 10 to 40, rlist from 1 to 1.028

 The number of OpenMP threads was set by environment variable
 OMP_NUM_THREADS to 48
 Using 1 MPI thread
 Using 48 OpenMP threads

 WARNING: Oversubscribing the available 24 logical CPU cores with 48 threads.
  This will cause considerable performance loss!

This suggests that HT is actually off as mdrun detects only 24 hardware threads!

--
Szilárd

 ---
 Program mdrun_d, VERSION 5.0.1
 Source code file:
 /export/data1/kho/software/gromacs5.1/gromacs-5.0.1/src/gromacs/mdlib/nbnxn_search.c,
 line: 2577

 Fatal error:
 48 OpenMP threads were requested. Since the non-bonded force buffer
 reduction is prohibitively slow with more than 32 threads, we do not allow
 this. Use 32 or less OpenMP threads.
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 so. i guess that is not a good idea.

 On Wed, Sep 10, 2014 at 9:55 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 that 8-20% performance increase was for gromacs 4.6.5

 On Wed, Sep 10, 2014 at 9:52 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Is it a good idea to use 48 OpenMP thread, under 1 MPI thread on 24 Xeon
 Processors?

 The mail list say such practice give about 8-20% performance increase

 Should I try g_tune_pme when I searched for imbalance in the log file
 and found nothing (24 OMP thread under 1 MPI thread on 24 Xeon Processor)?
 Or is that done automatically?

 Does gromacs support double precision calculation on GPU if the hardware
 supports that?

 The optimize fft option is also obsolete.

 Thanks again.



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Re: [gmx-users] Query regarding the addition of solvent molecule

2014-09-11 Thread Christina Florina

Hi,
 [ molecules ]
; Compound #mols
Protein_chain_A   1
CHX3414

 Here no water molecules to replace but to neutralize the system I
need to replace the solvent ions. As you told I went through the tutorial
regarding the genion and addition of ions, but to neutralize solvents apart
from water(SOL) I couldnt find enough details. I tried with methanol, then
I got Group 13 (MeOH) (instead of SOL) to replace the solvents with the
ions in the genion step. But with the solvents I am using like cyclohexane,
I am getting only 9 groups and if I try to choose any group its showing
error as follows:
*Your solvent group size (23449) is not a multiple of 8*
 I don't know how to resolve this error though I have modified the
topology file (.top) with the no. of ions. Kindly need help with this
issue. I have attached the screenshot of the error page in the link below.

https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0

Thank you.


On Tue, Sep 9, 2014 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 9/9/14 9:41 AM, Christina Florina wrote:

 Hi,
   Thank you for the suggestions. I did the modifications in the .itp
 file and the grompp step generated the .tpr file successfully.
   But now, I am facing problem in the genion step, while adding the NA
 ions the group 13 (usually SOL for water solvent) is not present there. If
 I select anyother group like system (Grp-1) its showing some fatal error
 which is not present in gromacs errors and documentation. I have attached
 the screenshot of the error page (terminal) and the new .itp file
 (modified) for your reference.
   Do I need to add the cyclohexane molecule (CHX) in any of the
 directories to resolve this error? Kindly need help.


 https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0


 There's no water in your system to replace:

 [ molecules ]
 ; Compound#mols
 Protein_chain_A 1
 CHX  3414

 I suggest you refer to some tutorial material to understand normal Gromacs
 workflows and topology organization.  There are many linked from the
 Gromacs website, some of which involve building system with
 complex/non-water solvents.


 -Justin

  On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 9/9/14 7:09 AM, Christina Florina wrote:

  Hi,
Thanks for your suggestions.
If the .itp file has error, is there any other way to generate
 .itp
 files for the solvents or do i need to write them manually? Because the
 .itp files I have attached are generated using PRODRG. If I edit the
 chx.itp file based on the corrections you have told, will it be fine? I
 am
 getting the same error for all the 4 solvent files I have generated
 using
 PRODRG. I do not get the .itp and .gro files online or tutorials for the
 organic solvents i am using for my md studies.


 The only problems I have ever had with PRODRG topologies are charges and
 charge groups.  If you fix those appropriately (charge groups being
 irrelevant if using the Verlet scheme in Gromacs), that's the only
 modification you should make.  I don't know where all that other stuff
 came
 from.

I have included the .itp file in both top directory and force
 field

 directory. It might be the reason the .gro file could be read in the
 solvate step. But how to make it in a correct format to proceed with?


 Solvation doesn't depend on your custom topologies at all.

I am new to gromacs using other organic solvents apart from water
 and

 default solvents in gromacs package. So, kindly need help how to build
 an
 .itp file and .gro file for a solvent and to resolve the issue.


  Make the changes I indicated in the last message.  Read Chapter 5 of
 the
 manual for explanations; all of the stuff I pointed out was either (1)
 syntactically incorrect or (2) not appropriate for the file format.

 -Justin


   On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote:




 On 9/9/14 12:51 AM, Christina Florina wrote:

   Hi,

  I have included the link to my dropbox where I have attached
 my
 gromacs topology files. Though I have included the cyclohexane itp
 file
 in
 the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO,
 Kindly need help in this regard.
  Thank you in advance.

 https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/
 AABxNv6VxA1gbSs7h2gkaIfxa?dl=0


   You have several problems:


 1. The #include statement for chx.itp is probably wrong (though I don't
 know how you're organizing your files), but unless you've put chx.itp
 in
 the force field directory, #include gromos43a1.ff/chx.itp is
 incorrect.

 2. The contents of chx.itp are wrong for several reasons.  The #ifndef
 lines are nonsensical and need to be deleted.  The #include statement
 for
 water needs to be deleted.  The [system] and [molecules] levels (which
 are
 system-level and thus can only go in a .top)

Re: [gmx-users] Query regarding the addition of solvent molecule

2014-09-11 Thread Justin Lemkul




On 9/11/14 8:49 AM, Christina Florina wrote:

Hi,
  [ molecules ]
; Compound #mols
Protein_chain_A   1
CHX3414

  Here no water molecules to replace but to neutralize the system I
need to replace the solvent ions. As you told I went through the tutorial
regarding the genion and addition of ions, but to neutralize solvents apart
from water(SOL) I couldnt find enough details. I tried with methanol, then
I got Group 13 (MeOH) (instead of SOL) to replace the solvents with the
ions in the genion step. But with the solvents I am using like cyclohexane,
I am getting only 9 groups and if I try to choose any group its showing
error as follows:
 *Your solvent group size (23449) is not a multiple of 8*
  I don't know how to resolve this error though I have modified the
topology file (.top) with the no. of ions. Kindly need help with this
issue. I have attached the screenshot of the error page in the link below.

https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0



The contents of ions.tpr do not appear to have CHX added.  Note that Protein 
and System have the same size.  Replacing CHX with ions is just like any other 
solvent (whether or not free ions would exist in a nonpolar solvent like this is 
another issue altogether).  You would choose CHX for replacement.  I suspect the 
.tpr file was constructed incorrectly or the topology is otherwise incorrect in 
its contents.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Contact angle measurement on a flat surface

2014-09-11 Thread Kester Wong

Hi Mark,Thank you for the information, that helps a lot!Binning the density profile seems to be the method of choice in quite a large number of papers published.Perhaps this method could be made into a GROMACS utility tool for future use? Thanks again Mark.Regards,Kester- 원본 메일 -보낸사람 : Mark Abraham mark.j.abra...@gmail.com받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2014년 9월 11일(목) 21:25:09제목 : Re: [gmx-users] Contact angle measurement on a flat surfaceHi,

Petter Johanson here in Berk's group does some similar things in a fairly
ad-hoc way (bin the density profile), but he suggests the methods here
http://www.mdpi.com/1099-4300/15/9/3734 might be useful.

Mark

On Wed, Sep 10, 2014 at 5:45 AM, Kester Wong wrote:

Dear all,

I would like to know what are the methods I could use to measure/plot the
contact angle of a water nanodroplet on flat graphene.

Is there a script or tool in GROMACS that can perform the contact angle
calculation?

I am aware that the commonly used Young's equation does not apply here,
since the droplet sizes will be in nanoscale.

The modified Young-Dupre's equation, and other plotting methods such as
the graphical binning approach by Werder et al. J. Phys. Chem. B 107,
1345-1352 (2003),

and the algorithm method by Ingebrigtsen and Toxvaerd, J. Phys. Chem. C
111, 8518 (2007) provided some theory on the calculation,

but I would like to know about the technical steps on doing the
measurement.

Any feedback is greatly appreciated.

Thank you in advance.

Regards,

Kester

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Re: [gmx-users] Net charge density distribution plots in GROMACS

2014-09-11 Thread soumadwip ghosh

Hi,
   Thanks for the reply. Tell me one of the 'other ways' you mentioned in
the reply. If you kindly check the link, I want to have a  net charge
distribution plot similar to that of figure 3.

Thanks in advance.
http://onlinelibrary.wiley.com/doi/10.1002/bip.22189/pdf
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Re: [gmx-users] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Johnny Lu

Ah. Thanks a lot.
As suggested by (
https://www.ibm.com/developerworks/community/blogs/brian/entry/linux_show_the_number_of_cpu_cores_on_your_system17?lang=en),

There are 12 real cores.
Type top and then press 1 sometimes give double the number of real cores,
but sometimes doesn't double the number (tested on different machines).

How to run an MPI rank per core ? By this way? OMP_NUM_THREADS=12
mdrun on a 12 core machine?

I tried openmp threads instead of mpi thread because gromacs wiki says
openmp threads are faster than mpi based parallelization.

from the gromacs wiki (
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI_and_OpenMP
):

In GROMACS 4.6 compiled with thread-MPI, OpenMP-only parallelization is the
default with Verlet scheme when using up to 8 cores on AMD platforms and up
to 12 and 16 cores on Intel Nehalem and Sandy Bridge, respectively. Note
that even running across two CPUs (in different sockets) on Intel platforms
OpenMP mutithreading is, in the majority of the cases, significantly faster
than MPI-based parallelization.

...

Assuming that there are N cores available, the following commands are
equivalent:

mdrun -ntomp N -ntmpi 1
OMP_NUM_THREADS=N mdrun
mdrun #assuming that N = 8 on AMD or N = 12/16 on Intel Nehalem/Sandy Bridge
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Re: [gmx-users] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Johnny Lu

The gromacs wiki also says that mixing mpi and openmp is bad on small
computers.

On Thu, Sep 11, 2014 at 9:44 AM, Johnny Lu johnny.lu...@gmail.com wrote:

Ah. Thanks a lot.
As suggested by (
https://www.ibm.com/developerworks/community/blogs/brian/entry/linux_show_the_number_of_cpu_cores_on_your_system17?lang=en),

There are 12 real cores.
Type top and then press 1 sometimes give double the number of real
cores, but sometimes doesn't double the number (tested on different
machines).

How to run an MPI rank per core ? By this way? OMP_NUM_THREADS=12
mdrun on a 12 core machine?

I tried openmp threads instead of mpi thread because gromacs wiki says
openmp threads are faster than mpi based parallelization.

from the gromacs wiki (
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI_and_OpenMP
):

In GROMACS 4.6 compiled with thread-MPI, OpenMP-only parallelization is
the default with Verlet scheme when using up to 8 cores on AMD platforms
and up to 12 and 16 cores on Intel Nehalem and Sandy Bridge, respectively.
Note that even running across two CPUs (in different sockets) on Intel
platforms OpenMP mutithreading is, in the majority of the cases,
significantly faster than MPI-based parallelization.

...

Assuming that there are N cores available, the following commands are
equivalent:

mdrun -ntomp N -ntmpi 1
OMP_NUM_THREADS=N mdrun
mdrun #assuming that N = 8 on AMD or N = 12/16 on Intel Nehalem/Sandy Bridge

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Re: [gmx-users] Hyper-threading Gromacs 5.0.1

2014-09-11 Thread Johnny Lu

this mail list thread talks about it:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg06331.html

On Thu, Sep 11, 2014 at 9:45 AM, Johnny Lu johnny.lu...@gmail.com wrote: