[gmx-users] Ion pair

[Tuanan Lourenço]

Hi everybody,

I am working with electrolytes simulations using Gromacs, so I am trying to
get the residence time (ion pair lifetime, ion cage lifetime) of the ions.
I tried to use gmx hbond with the option -contat, but if try get the acf of
the interaction the program always has a crash, I also have tried Travis
package, but the ACFs does not look nice in this application. So I am tring
to write my own code for this analysis but I have a dead line coming soon,
if some one know about a program in which I can do this analysis I will be
very glad.

Thank you

-- 
__
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE 
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[gmx-users] purpose of step pdb files during MD

[Vedat Durmaz]

hi guys,

from time to time i'm faced with GMX output files during MD called, e.g. in the 
current case:

step8164372b_n254.pdb
step8164372b_n2.pdb
step8164372c_n254.pdb
step8164372c_n2.pdb

what i know is that they are related to kind of exploding systems. however, i'm 
not really able to interpret their content. if i visualize them in VMD, i see a 
subset of my system surounded by explicit water molecules where the two *n254* 
files contain a larger part of my fibrils (polypeptides) than the *n2* files 
which only show few atoms of one particular amino acid. but if i pick certain 
atoms of the amino acids, they are often not correctly assigned to residue 
names and the atom index shown in VMD is different from the index listed in the 
underlying gro file.

where can i find detailed information about how to interpret the names and 
contents of these files? why are exactly these atoms written to the pdb files 
and what does the file name tell me?

any hint is appreciated.

many thanks,

vedat durmaz


-- 
Vedat Durmaz
Computational Molecular Design
Zuse Institute Berlin (ZIB)
Takustrasse 7
14195 Berlin, Germany
T: +49-30-84185-139
F: +49-30-84185-107
http://www.zib.de/durmaz


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Re: [gmx-users] gromacs ligand topology file for "GNP"

[Justin Lemkul]

On 9/6/17 3:46 PM, Deep kumar wrote:

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
 print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".



Does that make sense?  What is RND?


c) submitted the entry and after completion, downloaded the file as below:

 From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?



You don't need a .gro file to generate a position restraint file; as with most 
operations in GROMACS, you can use any coordinate file format here.  If you 
*really* want to use .gro, you can transform between formats with editconf.



And lastly, please let me know how to generate topology of "GNP" molecule
with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"



The error here is pretty clear.  You have a bad geometry for this molecule with 
a bond length that is about 3 times longer than it really should be. 
Visualizing the coordinates should make this apparent since ATB is telling you 
exactly which bond is problematic.


-Justin

--
==

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

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

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==
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[gmx-users] gromacs ligand topology file for "GNP"

[Deep kumar]

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".

c) submitted the entry and after completion, downloaded the file as below:

>From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?

And lastly, please let me know how to generate topology of "GNP" molecule
with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"

Thanks,
Deep
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Re: [gmx-users] Gromacs error: equilibration phase

[Deep kumar]

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".

c) submitted the entry and after completion, downloaded the file as below:

>From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html)
says, I have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?

Thanks,
Deep

On Tue, Sep 5, 2017 at 4:04 PM, Deep kumar 
wrote:

> Dear All,
>
> I have a query regarding Gromacs run. The error when running the
> "equilibration phase". I am following the tutorial from here:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/complex/06_equil.html
> 
>
> I am trying to prepare a system for MD run of 20ns for the pdb "4NYM". For
> the same I prepared two pdb files; 4NYM_clean.pdb (without ligands,
> GNP[ligand2.pdb] & RND[ligand3.pdb]) & 4NYM.pdb (with ligands). I produced
> the .itp and .gro files of the ligands separately using "prodrg"
> (attached). "posre_GNP.itp" & "posre_RND.itp" files were produced using
> gromacs tutorial by "gmx genrestr". All steps went well without error until
> the "nvt.mdp" equilibration run. I have attached the pdb files and the .mdp
> files I used. I have also attached a produced pdb (step0c.pdb) file just
> before the "nvt" crash/error.
>
> minim.mdp: is the file used to get "ions.tpr"
> em_real.mdp: for energy minimization
> nvt.mdp: for first equilibration phase
>
> The error I get is:
>
> [root@g ras-sos]# gmx mdrun -deffnm nvt
>
> :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
>
>
>
> GROMACS is written by:
>
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
>
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
>
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
>
> Dimitrios Karkoulis Peter Kasson Jiri 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 Tieleman Teemu Virolainen Christian Wennberg Maarten 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 5.1.4
>
> Executable: /usr/local/gromacs/bin/gmx
>
> Data prefix: /usr/local/gromacs
>
> Command line:
>
> gmx mdrun -deffnm nvt
>
>
>
>
>
> Back Off! I just backed up nvt.log to ./#nvt.log.6#
>
>
>
> Running on 1 node with total 4 cores, 4 logical cores
>
> Hardware detected:
>
> CPU info:
>
> Vendor: GenuineIntel
>
> Brand: Intel(R) Xeon(R) CPU E3-1220 v3 @ 3.10GHz
>
> SIMD instructions most likely to fit this hardware: AVX2_256
>
> SIMD instructions selected at GROMACS compile time: AVX2_256
>
>
>
> Reading file nvt.tpr, VERSION 5.1.4 (single precision)
>
> Changing nstlist from 10 to 25, rlist from 1.4 to 1.433
>
>
>
> Using 1 MPI thread
>
> Using 4 OpenMP threads
>
>
>
>
>
> Back Off! I just backed up nvt.trr to ./#nvt.trr.6#
>
>
>
> Back Off! I just backed up 

Re: [gmx-users] Ionic liquid simulation problem

[Ednilsom Orestes]

Hi Ghosh,

Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
species.
Now, should I use the same command to include the anionic species into the
box?

Best



*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
Cecília*
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*


2017-09-05 17:24 GMT-03:00 soumadwip ghosh :

> Hi,
>
> I am not sure why you used the gmx solvate command for putting the
> anionic species in your simulation box. It is meant for filling up the
> simulation box with water molceules as the resname 'SOL' in the
> topol.top file. Thus when you hit grompp it expects 'SOL' entry in
> your topology file, cant find it and prints an error. In my opinion,
> one should use the same gmx insert-molecules command for inserting the
> anionic part into the box. If you dont want to use water in the
> simulation you can proceed without the solvation step but cant use gmx
> solvate for inserting anionic species or anything else.
>
> Best
> Soumadwip Ghosh
> Post Doctoral Research Associate
> City of Hope Cancer Research Center
> Duarte 91010 CA
> USA
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[gmx-users] Modeling of the shear flow of the liquid using DEFORM

[Own 12121325]

Dear GROMACS users,

I would like to perform non-equilibrium simulation adding a shear flow on
the liquid in my bio-membrane system composed of lipids and water. By means
of the applications of the deformations I would like to shear a water in
X-Y dimensions along the surface of the membrane. Assuming that I make
modeling of the system in NPT ensemble with anisotropic coupling, will the
following options be correct for the setup?

compressibility = 0 0 4.5e-5 0.0 0.0 0.0 # here I sen compressibility for
all of the deformed directions xx, yy, xy etc to zero
ref_p   = 1.0135 1.0135 1.0135 0.0 0.0 0.0
; Deformation is on
Deform = 0 0 0 0.01 0.01 0.01 # here I add vel. 0.01 nm ps to the
non-diagonal elements corresponded to x and y dimensions of the box to
shear a liquid along it

Thanks so much for help!

Micky
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Re: [gmx-users] successive removal of position restrain?

[Justin Lemkul]

On 9/6/17 5:36 AM, Seera Suryanarayana wrote:

Dear gromacs users,

I have gone through one gromacs tutorial of md simulation in solvent. Where
they mentioned that successive removal of position restrain. In other words
first they have done NPT ensemble with 1000  1000  1000 energy constants,
then re executed the NPT ensemble with 100   100   100 energy constants and
finally third time they ran the NPT ensemble with 10   10   10 energy
constants. After this run they have stated the real MD production run with
position restraint. But I have done NPT ensemble only with 1000  1000 1000
force constant and then I removed the complete position restrains before MD
production run. My question comes here, Is there any difference between
their methodology and my methodology?



Well, naturally there is a difference, but whether or not it matters is a 
different question :)


I have never done step-wise removal of position restraints.  Some people swear 
by it.  Same story with warming a system from 0 K to a target temperature - I 
see no benefit but others believe it's necessary.  The purpose of equilibration 
is to relax the system and achieve a reasonably stable thermodynamic ensemble. 
If you've done that, proceed with your simulation.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] successive removal of position restrain?

[Wes Barnett]

On Wed, Sep 6, 2017 at 5:36 AM, Seera Suryanarayana 
wrote:

> Dear gromacs users,
>
> I have gone through one gromacs tutorial of md simulation in solvent. Where
> they mentioned that successive removal of position restrain. In other words
> first they have done NPT ensemble with 1000  1000  1000 energy constants,
> then re executed the NPT ensemble with 100   100   100 energy constants and
> finally third time they ran the NPT ensemble with 10   10   10 energy
> constants. After this run they have stated the real MD production run with
> position restraint. But I have done NPT ensemble only with 1000  1000 1000
> force constant and then I removed the complete position restrains before MD
> production run. My question comes here, Is there any difference between
> their methodology and my methodology?
>
> Thanks in advance
> Surya
> Graduate student
> India.
>

Hard to know since we don't know what your system is or why you are using
position restraints and then removing them. Have you contacted the author
of the tutorial?


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] GPU-accelerated performance

[Wes Barnett]

On Wed, Sep 6, 2017 at 4:58 AM, Alex  wrote:

> Hi all,
>
> We just got the new machines that were actually built with Szilárd's
> advice (a while back) and I am doing some preliminary tests. "My" machine
> has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan Xp
> GPUs. So far, I got good test system performance (~11K atoms, 92 ns/day)
> from '-nt 36' and running on all GPUs. Further increasing the number of
> threads only reduces performance. The test system is a CHARMM-based
> lipid+water setup, elongated in the Z-direction (6.7 nm x 6.7 nm x 11.2
> nm).Very decent performance (70 ns/day) for 16 CPU cores and two GPUs.
>
> Any suggestions on further increase what we can squeeze out of this thing
> for a single simulation? The relevant mdp section is below (CHARMM
> defaults, really). What would you try in your mdrun line?
>
> Thanks!
>
> Alex
>
> 
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> coulombtype = pme
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
>
>

You really just have to try different options for different systems. The
performance will be system-dependent. Expect larger systems to benefit more
from GPU acceleration. Try different combinations of MPI ranks and OMP
threads along with specifying the GPU's multiple times. I always do a
series of short runs with different combinations before choosing the
fastest one for a particular system and then doing a longer production run.
See http://www.gromacs.org/Documentation/Acceleration_and_parallelization

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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[gmx-users] HPC performance in Gromacs ?

[Li, J.]

Thanks, Pall,

I thought more threads will make the simulation faster. Is it not the case
for Gromacs?

I have tried to change the values. The file is provided here,
https://drive.google.com/a/rug.nl/file/d/0B-VoMAn-UrjYeko4d1VwUURCb00/view?usp=sharing
.

The command line is "gmx_mpi_d mdrun -s PE_pro_50s_npt5.tpr -v -deffnm
PE_pro_50s_npt5 -ntomp 1 -npme 18 -ntomp_pme 1 -nsteps 500 -pin on -dlb yes
-notunepme".

The performance is slower than before before and the imbalance is still
high. I don't know what it means.

Thanks in advance.
Best,
Jing




-- 
Jing Li
PhD student
FMNS, University of Groningen
Room 5115.0309, Nijenborg 4, Groningen
The Netherlands
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Re: [gmx-users] GPU-accelerated performance

[Nikhil Maroli]

First, take my wow!!! thats a huge system.

I would try the combinations of ntmpi XX and ntomp XXX for better
performance. Currently with 3 x GPU 1070 for ~11 K  system im getting
around 50 ns/day (12 core processor).

So I guess you can fly here. :)
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Re: [gmx-users] Error while running perl distances.pl

[Vytautas Rakeviius]

Well to better understand what is going on I suggest:* use strict; line tells 
to search for possible problems even if script can go on like it is.Maybe just 
remove it?
 * remove &>/dev/null or even better use other file instead of /dev/null like 
dump.txt
You will see it that system call is all OK from print to screen or to that file.
* Edit all open functions into open or die style. Example:open(OUT, 
">>summary_distances.dat") or die "can not open summary_distances.dat";If that 
file open call fails you will see error like you wrote.* Examine all files 
mentioned in script, they might be bad or not exist, that may hint to possible 
issues.
On Wednesday, September 6, 2017, 10:42:30 AM GMT+3, 가디 장데부 고라크스나트 
 wrote:  
 
 
Hello Vytautas,

I changed the script file to

gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'

 

rest is same

but it showed the same error as previous one.
Error readline() on closed filehandle IN at distances.pl line 16 Use of 
uminitialized value $distance in concatanation (.) or string at distances.pl 
line 30.
 

Could you help me out to solve this issue.

Dr. Changdev G. Gadhe

Post-Doc Researcher,

Convergence Research Center for Diagnosis, Treatment and Care System of 
Dementia,

Korea Institute of Science and Technology, 

Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea 

Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850

Email: f07...@kist.re.kr

 

 

 

 

---Original message---
From: "Vytautas Rakeviius "
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부 
고라크스나트
Cc.: gadhe.chang...@gmail.com
Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul)
Title: Re: [gmx-users] Error while running perl distances.pl
 

 
Script assumes that variable $distance is the second row separated by space in 
the file dist{number}.xvg which appears after execution of system callgmx 
distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select 
\'com of group \"lig\" plus com of group \"protein\"\'I just think that 
dist{number}.xvg creation fails for you in first place because "gmx distance" 
in the script is not adjusted according to your system.You use _mpi_d in your 
post.   On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 
 wrote:   Hello Gmx user,  I would like to transport solute 
molecule from the ion channel (intracellular to extracellular site) using 
steered MD and umbrella sampling method to calculate the energy. I followed Dr. 
Lemkul's tutorial and it works fine upto equilibration step but in distance.pl 
it shows some errors. I used the distance of pulling along the Z-axis but still 
it do not work. I found when I use distance as a pull-geometry, solute moves 
away from the channel rather transporting through channel. Then I tried 
direction as a pull-geoetry, then solute transported from the chanel,and 
generated pullf.xvg but not pullx.xvg file. I separated the trajectory using 
trjconv command gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o 
conf.gro -sep It generated conformations.Now I would like to calculate the 
COM distance between ion channel (protein) and solute (lig) using perl 
distance.pl but I received following error. Error readline() on closed 
filehandle IN at distances.pl line 16 Use of uminitialized value $distance in 
concatanation (.) or string at distances.pl line 30.Here is the distance.pl 
file which I used for this purpose which was downloaded from Dr. Lemkul's 
tutorial file. -#!/usr/bin/perl -w use strict; # loop g_dist 
command - measure distance in each frame, write to a filefor (my $i=0; $i<=800; 
$i++) {    print "Processing configuration $i...\n";    system("gmx distance -s 
md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of 
group \"lig\" plus com of group \"protein\"\' &>/dev/null");} # write output to 
single fileopen(OUT, ">>summary_distances.dat"); for (my $j=0; $j<=800; $j++) { 
   open(IN, "

[gmx-users] successive removal of position restrain?

[Seera Suryanarayana]

Dear gromacs users,

I have gone through one gromacs tutorial of md simulation in solvent. Where
they mentioned that successive removal of position restrain. In other words
first they have done NPT ensemble with 1000  1000  1000 energy constants,
then re executed the NPT ensemble with 100   100   100 energy constants and
finally third time they ran the NPT ensemble with 10   10   10 energy
constants. After this run they have stated the real MD production run with
position restraint. But I have done NPT ensemble only with 1000  1000 1000
force constant and then I removed the complete position restrains before MD
production run. My question comes here, Is there any difference between
their methodology and my methodology?

Thanks in advance
Surya
Graduate student
India.
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[gmx-users] GPU-accelerated performance

[Alex]

Hi all,

We just got the new machines that were actually built with Szilárd's 
advice (a while back) and I am doing some preliminary tests. "My" 
machine has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 
Titan Xp GPUs. So far, I got good test system performance (~11K atoms, 
92 ns/day) from '-nt 36' and running on all GPUs. Further increasing the 
number of threads only reduces performance. The test system is a 
CHARMM-based lipid+water setup, elongated in the Z-direction (6.7 nm x 
6.7 nm x 11.2 nm).Very decent performance (70 ns/day) for 16 CPU cores 
and two GPUs.


Any suggestions on further increase what we can squeeze out of this 
thing for a single simulation? The relevant mdp section is below (CHARMM 
defaults, really). What would you try in your mdrun line?


Thanks!

Alex


cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb    = 1.2
vdwtype = Cut-off
vdw-modifier    = Force-switch
rvdw_switch = 1.0
rvdw    = 1.2

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error while running perl distances.pl

[가디 장데부 고라크스나트]

Hello Vytautas,


I changed the script file to


gmx_mpi_d distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'





rest is same


but it showed the same error as previous one.


Error




readline() on closed filehandle IN at distances.pl line 16




Use of uminitialized value $distance in concatanation (.) or string at 
distances.pl line 30.





Could you help me out to solve this issue.



Dr. Changdev G. Gadhe

Post-Doc Researcher,


Convergence Research Center for Diagnosis, Treatment and Care System of 
Dementia,

Korea Institute of Science and Technology, 

Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea 

Ph.: +82-10-2779-1546 , Lab: +82-02-958-6850

Email: f07...@kist.re.kr










 


---Original message---
From: "Vytautas Rakeviius "
To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부 
고라크스나트
Cc.: gadhe.chang...@gmail.com
Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul)
Title: Re: [gmx-users] Error while running perl distances.pl








Script assumes that variable $distance is the second row separated by space in 
the file dist{number}.xvg which appears after execution of system call

gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg 
-select \'com of group \"lig\" plus com of group \"protein\"\'


I just think that dist{number}.xvg creation fails for you in first place 
because "gmx distance" in the script is not adjusted according to your system.

You use _mpi_d in your post.












On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 
 wrote:











Hello Gmx user,







I would like to transport solute molecule from the ion channel (intracellular 
to extracellular site) using steered MD and umbrella sampling method to 
calculate the energy.




I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but 
in distance.pl it shows some errors.




I used the distance of pulling along the Z-axis but still it do not work. I 
found when I use distance as a pull-geometry, solute moves away from the 
channel rather transporting through channel. Then I tried direction as a 
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg 
but not pullx.xvg file.




I separated the trajectory using trjconv command




gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep




It generated conformations.













Now I would like to calculate the COM distance between ion channel (protein) 
and solute (lig) using perl distance.pl but I received following error.




Error





readline() on closed filehandle IN at distances.pl line 16




Use of uminitialized value $distance in concatanation (.) or string at 
distances.pl line 30.













Here is the distance.pl file which I used for this purpose which was downloaded 
from Dr. Lemkul's tutorial file.




-

#!/usr/bin/perl -w




use strict;




# loop g_dist command - measure distance in each frame, write to a file

for (my $i=0; $i<=800; $i++) {

print "Processing configuration $i...\n";

system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\' 
&>/dev/null");

}




# write output to single file

open(OUT, ">>summary_distances.dat");




for (my $j=0; $j<=800; $j++) {

open(IN, "