[gmx-users] gromacs

[Abid Channa]

Hi gromacs users,

I am working on Sotase A complex simulation, I have done 5 ns simulation,
I want to extend simulatiom from 5 to 10 ns, is there any person tell me
extending command quickly? Thanks in advance for Justin Lemkul



Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051  
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[gmx-users] Gromacs

[Dilip H N]

Hello ,

While creating the topology fie from the perl interpreter, the topology
file is created and a file selection_atoms_raw file is also created..??
hw is this possible..?? hope that is wrong.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.



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[gmx-users] Gromacs

[Dilip H N]

i have a molecule of an acid...
how can i create a topology file from that and do the simulation..??
i cant use gmx pdb2gmx -f file.pbd -o file.gro 
since it asks force feild , and thn water model..??
i dont want water to be added (since it is asking water model)...
how can i proceed with my acid molecule for simulation..??

Thank you...

-- 
With Best Regards,





 Sent with Mailtrack

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[gmx-users] gromacs

[Meenakshi Rajput]

hi gromacs users
I have done the whole mdrun simulation of my protein human serum albumin
complex with ligand and i got all the files. But when i opened the pdb file
obtained after md simulation in pymol to see the interaction, ligand went
to some other place. It was not in the active site. please tell me what is
the problem, where i m wrong?
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[gmx-users] gromacs

[Meenakshi Rajput]

hello users
Can anyone tell me that is it necessary to run a long simulation at one
tme? or I can do it in parts. Like if i am doing for 1000ps, can i do 500
at one tme and rest in next run? Would it give same results or its a wrong
procedure?
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[gmx-users] gromacs

[Meenakshi Rajput]

i used the pdb2gmx command but i get a message "command not found". can you
help me
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Re: [gmx-users] gromacs

[Christopher Neale]

(A) modify your .mdp to increase nsteps and then make a new .tpr, then run 
mdrun -cpi my.cpt files and use the new .tpr file.
(B) use tpbconv to modify your original .tpr file and then rerun using mdrun 
-cpi
(C) simply run as before (though you need -cpi option to mdrun since it is a 
restart) and give mdrun also the option -nsteps (where 250 new steps should 
give you an additional 5 ns if your timestep is 2 ps).



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Abid Channa 

Sent: 12 February 2015 23:56
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: gmx-us...@gromacs.org
Subject: [gmx-users] gromacs

Hi gromacs users,

I am working on Sotase A complex simulation, I have done 5 ns simulation,
I want to extend simulatiom from 5 to 10 ns, is there any person tell me
extending command quickly? Thanks in advance for Justin Lemkul



Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051
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Re: [gmx-users] gromacs

[Abid Channa]

thanks Christopher Neale for your suggestion , I have done my simulation 
successfully

Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051
> From: chris.ne...@alum.utoronto.ca
> To: gmx-us...@gromacs.org
> Date: Fri, 13 Feb 2015 05:28:09 +
> Subject: Re: [gmx-users] gromacs
> 
> (A) modify your .mdp to increase nsteps and then make a new .tpr, then run 
> mdrun -cpi my.cpt files and use the new .tpr file.
> (B) use tpbconv to modify your original .tpr file and then rerun using mdrun 
> -cpi
> (C) simply run as before (though you need -cpi option to mdrun since it is a 
> restart) and give mdrun also the option -nsteps (where 250 new steps 
> should give you an additional 5 ns if your timestep is 2 ps).
> 
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Abid Channa 
> 
> Sent: 12 February 2015 23:56
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: gmx-us...@gromacs.org
> Subject: [gmx-users] gromacs
> 
> Hi gromacs users,
> 
> I am working on Sotase A complex simulation, I have done 5 ns simulation,
> I want to extend simulatiom from 5 to 10 ns, is there any person tell me
> extending command quickly? Thanks in advance for Justin Lemkul
> 
> 
> 
> Abid Ali Channa,
> Junior Research Fellow,
> Lab No.  P-133, Computational Chemistry Unit,
> Dr .Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi-75270.
> Karachi-Pakistan.
> UAN # (92-21) 111-222-292 Ext. (309)
> Cell # +923013553051
> --
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Re: [gmx-users] gromacs

[Alexander Law]

Add: "-cpi state.cpt" to your command line. And change your .mpd file to 
reflect the time you want to use.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Abid Channa 
[abid.cha...@hotmail.com]
Sent: Friday, February 13, 2015 5:56 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: gmx-us...@gromacs.org
Subject: [gmx-users] gromacs

Hi gromacs users,

I am working on Sotase A complex simulation, I have done 5 ns simulation,
I want to extend simulatiom from 5 to 10 ns, is there any person tell me
extending command quickly? Thanks in advance for Justin Lemkul



Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051
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Re: [gmx-users] gromacs

[Abid Channa]

Thanks Alexander Law for your suggestion 

Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi-75270.
Karachi-Pakistan.
UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051


> Date: Fri, 13 Feb 2015 05:00:19 +
> From: alexander@pg.canterbury.ac.nz
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs
> 
> Add: "-cpi state.cpt" to your command line. And change your .mpd file to 
> reflect the time you want to use.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Abid Channa 
> [abid.cha...@hotmail.com]
> Sent: Friday, February 13, 2015 5:56 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Cc: gmx-us...@gromacs.org
> Subject: [gmx-users] gromacs
> 
> Hi gromacs users,
> 
> I am working on Sotase A complex simulation, I have done 5 ns simulation,
> I want to extend simulatiom from 5 to 10 ns, is there any person tell me
> extending command quickly? Thanks in advance for Justin Lemkul
> 
> 
> 
> Abid Ali Channa,
> Junior Research Fellow,
> Lab No.  P-133, Computational Chemistry Unit,
> Dr .Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi-75270.
> Karachi-Pakistan.
> UAN # (92-21) 111-222-292 Ext. (309)
> Cell # +923013553051
> --
> 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.
> 
> This email may be confidential and subject to legal privilege, it may
> not reflect the views of the University of Canterbury, and it is not
> guaranteed to be virus free. If you are not an intended recipient,
> please notify the sender immediately and erase all copies of the message
> and any attachments.
> 
> Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more
> information.
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[gmx-users] Gromacs Error

[manoj damale]

Dear All,
i'm geting below error while subjecting my system (Protein-ligand) for 
equlibriation in nvt.mdp file

mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p 
topol.top -n index.ndx -o nvt.tpr 
 :-)  G  R  O  M  A  C  S  (-:

   GRowing Old MAkes el Chrono Sweat

    :-)  VERSION 4.5.3  (-:

    Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
    Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
    Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
    Copyright (c) 2001-2010, The GROMACS development team at
    Uppsala University & The Royal Institute of Technology, Sweden.
    check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

    :-)  grompp  (-:

Option Filename  Type Description

  -f    nvt.mdp  Input    grompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c em.gro  Input    Structure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt!  Index file
  -p  topol.top  Input    Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o    nvt.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-nice    int    0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-time    real   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
    sites
-maxwarn int    0   Number of allowed warnings during input processing
-[no]zero    bool   no  Set parameters for bonded interactions without
    defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
    atomtypes

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#

ERROR 1 [file nvt.mdp]:
  With coulombtype = PME-Switch, rcoulomb must be <= rlist

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'UNT'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Setting gen_seed to 3507
Velocities were taken from a Maxwell distribution at 300 K

---
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Yeah, a Wuzz, Or a Jerk" (F. Black)
 With Best Regards.

Mr.Manoj Damale,
M.S. Pharma (Pharmacoinformatics) NIPER,
Kolkata, West Bengal State,
India.
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[gmx-users] Gromacs Path

[Live King]

Hi Everyone,

I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs,
then what is path of my Gromacs directory ? I don't seem to find it
anywhere .

Thanks,
vikas
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Re: [gmx-users] Gromacs

[saranya]

GROMACS users,

I was trying to perform a MD simulation of a system with a protein with Ag+
metal ion but realized that GROMACS does not  have parameters for the Ag+
ion. I tried to include the parameters in the ion.itp file but did not
succeed yet. Does anyone knows the right procedure to introduce this ions
into the file ions.itp? do we have to change anything more in order to
GROMACS recognize the new ion?

With Regards

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] Gromacs

[Ebert Maximilian]

Maybe you should start telling is which force field you are trying to use. 
GROMACS provides 15 different.

Max

> On Oct 6, 2015, at 1:51 AM, saranya  wrote:
> 
> GROMACS users,
> 
> I was trying to perform a MD simulation of a system with a protein with Ag+
> metal ion but realized that GROMACS does not  have parameters for the Ag+
> ion. I tried to include the parameters in the ion.itp file but did not
> succeed yet. Does anyone knows the right procedure to introduce this ions
> into the file ions.itp? do we have to change anything more in order to
> GROMACS recognize the new ion?
> 
> With Regards
> 
> *Saranya Vasudevan,*
> 
> *Research Scholar,*
> 
> *Molecular Quantum Mechanics Laboratory,*
> 
> *Department of Physics,*
> 
> *Bharathiar University,*
> 
> *Coimbatore-46*
> -- 
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Re: [gmx-users] Gromacs

[saranya]

i tried to run in OPLSAA force field sir.


*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*

On Tue, Oct 6, 2015 at 7:39 PM, Ebert Maximilian 
wrote:

> Maybe you should start telling is which force field you are trying to use.
> GROMACS provides 15 different.
>
> Max
>
> > On Oct 6, 2015, at 1:51 AM, saranya  wrote:
> >
> > GROMACS users,
> >
> > I was trying to perform a MD simulation of a system with a protein with
> Ag+
> > metal ion but realized that GROMACS does not  have parameters for the Ag+
> > ion. I tried to include the parameters in the ion.itp file but did not
> > succeed yet. Does anyone knows the right procedure to introduce this ions
> > into the file ions.itp? do we have to change anything more in order to
> > GROMACS recognize the new ion?
> >
> > With Regards
> >
> > *Saranya Vasudevan,*
> >
> > *Research Scholar,*
> >
> > *Molecular Quantum Mechanics Laboratory,*
> >
> > *Department of Physics,*
> >
> > *Bharathiar University,*
> >
> > *Coimbatore-46*
> > --
> > 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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Re: [gmx-users] Gromacs

[saranya]

Respected Sir,
  Though im finshed upto production step of protein metal
complexes, topology file couldnt be created and there is no information
about any atoms in my pdb file.  the created topology file are shown below


;
;File 'ebolaag.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Wed Oct  7 16:06:22 2015
;
;This is a standalone topology file
;
;It was generated using program:
;pdb2gmx_d - VERSION 4.5
;
;Command line was:
;./pdb2gmx_d -f ebolaag.pdb -o ebolaag.gro -p ebolaag.top -ignh
;
;Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "ebolaag_Protein_chain_A.itp"
#include "ebolaag_Ion_chain_A2.itp"

; Include water topology
#include "oplsaa.ff/tip4p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "oplsaa.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Ion_chain_A21
SOL  4673



I can't understand what is the problem, so pls tell me  what could be the
reason for this.


Sincierly,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] Gromacs

[soumadwip ghosh]

Hi,
   How is it possible that you have finished up to production run without
the .top file ? The first line of your ebolaag.top says that the topology
has been generated. How have you been doing any of the equilibration steps
without the .top file? Information regarding atoms are there in the
ebolaag_Protein_chain_A.itp
and the ebolaag_Ion_chain_A2.itp files created by pdb2gmx. Your comments do
not make any sense to me.

Soumadwip
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[gmx-users] gromacs error

[Puneet]

Hello 

 

I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error ? 

 

Error

 

Program grompp, version 3.3.3

source code file: toppush.c, line: 1396

 

Fatal error:

No such moleculetype NA

 

Please reply as soon as possible its really urgent for me.

 

Regards

Puneet Kaur

 

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[gmx-users] Gromacs Tutorial

[Tsjerk Wassenaar]

Hey :)

As some of you know, some years ago I developed an extensive Gromacs
tutorial (at the University of Utrecht). That work has caught they eye of
educators, and now the tutorial is published as an educational paper! Just
kind of funny that I'm not an author.
For those interested:

http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract

Enjoy!

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] Gromacs Tutorial

[João Rodrigues]

Dear all,

Those of you who read the paper will realize that we do acknowledge Tsjerk,
and keep doing so on the web pages of the material, but there are reasons
we considered sufficient to justify the author listing on the paper.

However, since Tsjerk knows me and the other authors (them actually rather
well) since at least 2008, I (we) will sort this issue privately.

Cheers,

João
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[gmx-users] Gromacs issue

[khourshaeishargh]

 Dear All

I have a quick question about GROMACS. Is there any chance to exert
different types of loading such as torsional or bending or linear tension
loading on simulation box in GROMACS ?

Best wishes

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran
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[gmx-users] Gromacs issue

[khourshaeishargh]

 Dear All

I have a quick question about GROMACS. Is there any chance to exert
different types of loading such as torsional or bending or linear tension
loading on simulation box in GROMACS ?

Best wishes

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran
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[gmx-users] Gromacs Installation

[ABANTIKA PAL]

Hi,

I have installed GROMACS 5.1.2 by performing the steps described in the 
installation guide. All the steps have been executed successfully. But, no 
executable of mdrun is  created in the build folder. Moreover, upon executing 
"which gromacs", its showing 
 no gromacs in 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.

Thanks and regards

Abantika
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[gmx-users] Gromacs installation.

[Elsaid Younes]

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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[gmx-users] gromacs installation

[roshanak starlight]

hello
i try to install gromacs in my laptop with this cpu :AMD Dual-core
processor E-350 and Linux operating system ubuntu 14.04
i installed gromacs-5.1.2  and gromacs-5 but both of  these versions get
error about grompp .and installation from software center (gromacs-4.5.6)
get this error: illegal instruction core dumped .
Who knows what's the problem?

one told me that :I think you would run gmx under admin or force UBUNTU to
set gromacs in your path
what shuld i do?
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[gmx-users] GROMACS mdrun

[Shilpa Janarthanan]

Hi,
While running an MD job for 10 ns, the system restarts in the final step of
MD (mdrun -v -deffnm md)
This happens continuously, and the data are not generated.
What system settings should I make, to make it run continuously until
finishing all the steps?

Thank you.

-- 
Shilpa J
Department of Bioinformatics,
SASTRA University.
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[gmx-users] Gromacs Learning

[Sheikh Imamul Hossain]

Hi all,
I am very very new in gromacs. My first project is to simulate dppc lipids
with water by using coarse grained model. Then I have the plan to add
cholesterol and proteins into my system. Can anyone suggest me how can I
start ? How can I edit pdb files? Which sites will be helpful to me. I have
installed gromacs 5.0.7 and vmd. I have started gromacs tutorials ..Bevan
Lab.

Thanks in advance
Imamul
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Re: [gmx-users] Gromacs

[David van der Spoel]

On 12/01/17 10:11, Dilip H N wrote:

i have a molecule of an acid...
how can i create a topology file from that and do the simulation..??
i cant use gmx pdb2gmx -f file.pbd -o file.gro 
since it asks force feild , and thn water model..??
i dont want water to be added (since it is asking water model)...
how can i proceed with my acid molecule for simulation..??

Thank you...


What acid?

Maybe you should rad chapter 5 of the manual, run a few tutorials and 
then head over to http://virtualchemistry.org


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] gromacs ettor

[chemocev marker]

Hi
I am using gromacs and facing this error

In tMPI thread #16: Affinity setting failed. This can cause performance
degradation.

can you tell me why is actually this,
best

Abdul
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[gmx-users] gromacs development

[Tomislav Jurin]

Hi,
my name is Tomislav, 25 years old, software developer from Croatia, Split. I am 
mostly Java developer, but with high interest in C/C++ to which I was 
introduced in college while working on small embedded projects (mostly arduino 
and similar stuff ). My first encounter with gromacs was when my gaming 
computer was used as work station for one physics project, which ended pretty 
badly for my gaming career (tl,dr: computer too busy to run anything but 
gromacs ) :).
I have basic understanding of C++ (worked some short time as c++ developer for 
embedded projects ) but lately I have been mostly on Java so I will have to do 
some "warm up" from my side.
If you have any advices how to start, or even some beginner friendly task to 
work on, I am highly interested on taking it.

Best regards,Tomislav
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[gmx-users] gromacs paper

[Tomaz Zorec]

Hi,

does anyone have a copy of this conference paper / the conference
proceedings book (below)? If so would you be so kind to mail it to me (copy
or similar)?

"Bekker, H., Berendsen, H. J. C., Dijkstra, E. J., Achterop, S., van
Drunen, R., van der
Spoel, D., Sijbers, A., Keegstra, H., Reitsma, B., Renardus, M. K. R.
Gromacs: A parallel
computer for molecular dynamics simulations. In Physics Computing 92
(Singapore, 1993).
de Groot, R. A., Nadrchal, J., eds. . World Scientific."

Thank you very much!

Best,

Tomaž
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[gmx-users] gromacs Bug?

[ANDRES ADOLFO ORTEGA GUERRERO]

Hi dear Gromacs  users, i would like to report something maybe could be a
bug or a mistake of me , you´ll see, i run an MD of a System with CNT
Protein Water and ions, i use a index.ndx file, my CNT doestn´t have any
charges, but when i check the Coul SR CNT-CNT there were really huge,

so i start a process and run different MD in order to get the problem, and
, the only way i could Coul SR CNT-CNT 0 as is supposed to be, was when i
do not use an index file,
with different simulation where i use the index.ndx file, my energy are
different ,

Thank You

Andres
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Re: [gmx-users] gromacs

[HANNIBAL LECTER]

Do you know why are you even performing MD Simulation? Do you even know
what it means? Do you know what to expect?


On Thu, Jul 31, 2014 at 1:16 AM, Meenakshi Rajput 
wrote:

> hi gromacs users
> I have done the whole mdrun simulation of my protein human serum albumin
> complex with ligand and i got all the files. But when i opened the pdb file
> obtained after md simulation in pymol to see the interaction, ligand went
> to some other place. It was not in the active site. please tell me what is
> the problem, where i m wrong?
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Re: [gmx-users] gromacs

[Justin Lemkul]

On 7/31/14, 1:16 AM, Meenakshi Rajput wrote:

hi gromacs users
I have done the whole mdrun simulation of my protein human serum albumin
complex with ligand and i got all the files. But when i opened the pdb file
obtained after md simulation in pymol to see the interaction, ligand went
to some other place. It was not in the active site. please tell me what is
the problem, where i m wrong?



Most likely a periodicity effect.  Re-image with trjconv.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-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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[gmx-users] gromacs error

[Urszula Uciechowska]

Dear Gromacs users,


I tried to run coarse grained MD however after a few steps I got:
Step 39, time 0.78 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  10457  10459   89.80.3107   0.8288  0.3100
  10459  10463   90.30.3075   1.0108  0.3100
  10463  10467   90.60.3084   0.8774  0.3100
  10467  10469   81.10.3103   0.3823  0.3100
  10469  10471   90.30.3121   0.1885  0.3100
Wrote pdb files with previous and current coordinates

Step 40, time 0.8 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 165002.767686, max 10334958.00 (between atoms 10457 and 10459)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  10443  10445   30.10.3100   0.3581  0.3100
  10445  10447  102.20.3102 266.6146  0.3100
  10447  10450   59.30.3100 624.1382  0.3100
  10450  10452  101.40.3105 5390.4609  0.3100
  10452  10454   87.90.3083 104154.3047  0.3100
  10454  10457   83.90.3497 439143.5312  0.3100
  10457  10459   87.50.8288 3203837.2500  0.3100
  10459  10463   87.81.0108 2960821.2500  0.3100
  10463  10467   95.20.8774 763857.8125  0.3100
  10467  10469   95.50.3823 195859.2656  0.3100
  10469  10471  104.30.1885 43565.4141  0.3100
  10471  10473   90.30.3534 7857.3394  0.3100
  10473  10475  105.50.3125  57.7529  0.3100
  10475  10477   90.00.3099   0.3849  0.3100
  10477  10480   32.40.3101   0.3647  0.3100
Wrote pdb files with previous and current coordinates
mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
mpiexec: kill_others_now: alarm went off, killing all other tasks.
mpiexec: kill_tasks: killing all tasks.
mpiexec: process_kill_event: evt 10 task 1 on wn350.
mpiexec: process_kill_event: evt 12 task 3 on wn501.
mpiexec: process_kill_event: evt 11 task 2 on wn350.
mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).

in log file last line is:

Constraining the starting coordinates (step 0)

Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.04e-06
Initial temperature: 1.8161e-07 K

Started mdrun on node 0 Wed Jul 30 10:39:50 2014

   Step   Time Lambda
  00.00.0

Grid: 42 x 42 x 42 cells
   Energies (kJ/mol)
   Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)
6.24872e+031.47844e+041.75778e+034.11810e+02   -2.32179e+07
   Coulomb (SR) Position Rest.  PotentialKinetic En.   Total Energy
   -4.49776e+032.00073e-01   -2.31992e+071.44043e+01   -2.31992e+07
Temperature Pressure (bar)   Constr. rmsd
1.55259e-03   -1.41563e+035.56533e-06

my input file:

define   =  -DPOSRES
dt   =  0.02
nsteps   =  25000
nstxout  =  0
nstvout  =  0
nstlog   =  100
nstxtcout=  100
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein W
tau-t=  1.0 1.0
ref-t=  300 300
Pcoupl   =  Berendsen
Pcoupltype   =  isotropic
tau-p=  12.0
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  com

What is wrong here?

best regards
Urszula Uciechowska


-
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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[gmx-users] Gromacs help

[Tuhin Samanta]

Dear,
Please tell me how i will use g_select command as i am simulating only
water molecules not any other reference molecule is there in my system but
i want to select a water molecule, and chose all water molecule within 0.4
nm around it, can you please tell me the proper command as i am getting
error with this command-

 g_select -f npt_ir.gro -s npt_ir.tpr - select '"Nearby water" resname SOL
and within 0.4 ' -n indexg1.ndx -on indextrial.ndx
eroor message  is that :

Invalid command line argument:
-
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Tuhin Samanta
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Re: [gmx-users] gromacs

[rajat desikan]

Hi,
There is no problem in doing the simulation in parts as long as you
take care to ensure continuity by using .cpt files, etc. You can
concatenate the trajectory in the end for analysis.
Regards,

On 8/30/14, Meenakshi Rajput  wrote:
> hello users
> Can anyone tell me that is it necessary to run a long simulation at one
> tme? or I can do it in parts. Like if i am doing for 1000ps, can i do 500
> at one tme and rest in next run? Would it give same results or its a wrong
> procedure?
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] gromacs error

[Yaser Hosseini]

hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:


gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
 Command 'gcx' from package 'gcx' (universe)
 Command 'ngmx' from package 'gromacs' (universe)
 Command 'gm' from package 'graphicsmagick' (universe)
 Command 'gmt' from package 'libgenome-perl' (universe)
gmx: command not found


and other problem :

solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
solvate: command not found

thank you for your help.
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[gmx-users] gromacs installation

[Amir Khan]

Dear Gromacs users

I install gromacs version 5.0.2 by this command line:cmake .. 
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

but I received an error that showed regression tests and it's link is inactive.


please help me , how can I install gromacs without regression test by cmake?


thanks alot

 
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[gmx-users] gromacs installation

[Amir Khan]

Dear Gromacs users

I install gromacs version 5.0.2 by this command line:cmake .. 
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

but I received an error that showed regression tests and it's link is inactive.


please help me , how can I install gromacs without regression test by cmake?


thanks alot

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[gmx-users] Gromacs-fda

[Lod King]

Hi amber users
I am trying to analyze protein pairwise-forces for my protein. After
getting some files and running the following commands:

$ gmx_fda editconf -f 300.pdb -o pdb.gro
$ gmx_fda grompp -f test.mdp -c pdb.gro -p gromacs.top -o water.tpr
-maxwarn 5
$ gmx_fda make_ndx -f water.tpr

$ gmx_fda mdrun -nt 1 -rerun 1wq5_6.1.trr -pfi test.pfi -pfn index.ndx -s
water.tpr -pfa output.pfa -pfr output.pfr

I obtained index.ndx, output.pfa and out.pfr files.

In my pfr file, it shows the output with:

pairwise_forces_scalar
frame 0
0 5 3.390778e+01 48
0 4 2.046505e+00 48
0 6 -1.183681e+00 48
0 1 -1.727842e+01 112
0 2 -3.984052e+00 48
0 3 -2.990689e+00 48
0 146 4.887157e-01 48
0 148 -4.024438e-01 48
0 123 -9.690338e-01 48
0 118 -4.066894e-01 48

1. what do "48, 112" mean in my file?

2. I also attached the "test.mdp, and test.pfi" files I downloaded from the
web page, I wonder are these two files applied to all or should I be aware
of selecting them specifically?

3. during the step in generating index.ndx, I was asked to select:

0 System
  1 Protein
  2 Protein-H
  3 C-alpha
  4 Backbone
  5 MainChain
  6 MainChain+Cb
  7 MainChain+H
  8 SideChain

but after selecting 1, it generated all info including 0, 1, 2,
3index..Do I have to make script to select only 1:protein? (index
attached too)

Three question, any answer would help..

#For .mdp

(; Run parameters
integrator= md
nsteps  = 50;
dt= 0.002; 2 fs
; Output control
nstxout = 1;
nstvout = 1;
nstfout= 0;
nstxtcout= 1000;
;nstxout-compressed = 1000;
nstenergy= 1000;
nstlog= 1;
; Constraints
constraint_algorithm = lincs;
constraints= hbonds; d
lincs_iter= 1;
lincs_order= 4;
continuation= yes;
; Neighborsearching
cutoff-scheme   = Verlet;
verlet-buffer-tolerance = 0.005;
ns_type = grid  ;
nstlist = 20;
rlist= 1.0;
rcoulomb= 1.0;
rvdw= 1.0;
; Electrostatics
coulombtype= PME;
pme_order= 4;
fourierspacing= 0.16;
; Temperature coupling is on
tcoupl= V-rescale;
tc-grps= System;
tau_t= 0.1;
ref_t= 298;
pcoupl= Parrinello-Rahman;
pcoupltype= isotropic;
tau_p= 2.0;
ref_p= 1.0;
compressibility = 4.5e-5;
pbc= xyz;
DispCorr= EnerPres;
gen_vel= no
pull= no  )

#For .psi

(onepair = summed
group1 =  Protein
group2 =  Protein
atombased = pairwise_forces_scalar
residuebased = pairwise_forces_scalar
type =  nonbonded
time_averages_period = 0)
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[gmx-users] GROMACS Infrastructure

[Nam Pho]

Hello GROMACS Users,

My name is Nam and I support a campus supercomputer for which one of the
major applications is GROMACS. I was curious if anyone has optimized
servers for cost and has a blueprint for that, what servers and
configurations are ideal for cost and performance?

--

Nam Pho

Director for Research Computing
University of Washington
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[gmx-users] gromacs performance

[Carlos Rivas]

Hey guys,
Anybody running GROMACS on AWS ?

I have a strong IT background , but zero understanding of GROMACS or OpenMPI. ( 
even less using sge on AWS ),
Just trying to help some PHD Folks with their work.

When I run gromacs using Thread-mpi on a single, very large node on AWS things 
work fairly fast.
However, when I switch from thread-mpi to OpenMPI even though everything's 
detected properly, the performance is horrible.

This is what I am submitting to sge:

ubuntu@ip-10-10-5-81:/shared/charmm-gui/gromacs$ cat sge.sh
#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -e out.err
#$ -o out.out
#$ -pe mpi 256

cd /shared/charmm-gui/gromacs
touch start.txt
/bin/bash /shared/charmm-gui/gromacs/run_eq.bash
touch end.txt

and this is my test script , provided by one of the Doctors:

ubuntu@ip-10-10-5-81:/shared/charmm-gui/gromacs$ cat run_eq.bash
#!/bin/bash
export GMXMPI="/usr/bin/mpirun --mca btl ^openib 
/shared/gromacs/5.1.5/bin/gmx_mpi"

export MDRUN="mdrun -ntomp 2 -npme 32"

export GMX="/shared/gromacs/5.1.5/bin/gmx_mpi"

for comm in min eq; do
if [ $comm == min ]; then
   echo ${comm}
   $GMX grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c 
step5_charmm2gmx.pdb -p topol.top
   $GMXMPI $MDRUN -deffnm step6.0_minimization

fi

if [ $comm == eq ]; then
  for step in `seq 1 6`;do
   echo $step
   if [ $step -eq 1 ]; then
  echo ${step}
  $GMX grompp -f step6.${step}_equilibration.mdp -o 
step6.${step}_equilibration.tpr -c step6.0_minimization.gro -r 
step5_charmm2gmx.pdb -n index.ndx -p topol.top
  $GMXMPI $MDRUN -deffnm step6.${step}_equilibration
   fi
   if [ $step -gt 1 ]; then
  old=`expr $step - 1`
  echo $old
  $GMX grompp -f step6.${step}_equilibration.mdp -o 
step6.${step}_equilibration.tpr -c step6.${old}_equilibration.gro -r 
step5_charmm2gmx.pdb -n index.ndx -p topol.top
  $GMXMPI $MDRUN -deffnm step6.${step}_equilibration
   fi
  done
fi
done




during the output, I see this , and I get really excited, expecting blazing 
speeds and yet, it's much worse than a single node:

Command line:
  gmx_mpi mdrun -ntomp 2 -npme 32 -deffnm step6.0_minimization


Back Off! I just backed up step6.0_minimization.log to 
./#step6.0_minimization.log.6#

Running on 4 nodes with total 128 cores, 256 logical cores, 32 compatible GPUs
  Cores per node:   32
  Logical cores per node:   64
  Compatible GPUs per node:  8
  All nodes have identical type(s) of GPUs
Hardware detected on host ip-10-10-5-89 (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2686 v4 @ 2.30GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
Number of GPUs detected: 8
#0: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#1: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#2: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#3: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#4: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#5: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#6: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#7: NVIDIA Tesla V100-SXM2-16GB, compute cap.: 7.0, ECC: yes, stat: 
compatible

Reading file step6.0_minimization.tpr, VERSION 5.1.5 (single precision)
Using 256 MPI processes
Using 2 OpenMP threads per MPI process

On host ip-10-10-5-89 8 compatible GPUs are present, with IDs 0,1,2,3,4,5,6,7
On host ip-10-10-5-89 8 GPUs auto-selected for this run.
Mapping of GPU IDs to the 56 PP ranks in this node: 
0,0,0,0,0,0,0,1,1,1,1,1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,5,5,5,5,5,5,5,6,6,6,6,6,6,6,7,7,7,7,7,7,7



Any suggestions? Greatly appreciate the help.


Carlos J. Rivas
Senior AWS Solutions Architect - Migration Specialist

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[gmx-users] gromacs instillation

[Ali Ahmed]

Hello GMX users
I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
2019.1.
When I open a new terminal and hit gmx, it says gromacs is currently not
installed. You can install it by typing:  sudo apt install gromacs. When I
did it, the version became 5.1.2.

Any idea how to solve it!

Thank you
Ali
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[gmx-users] Gromacs error

[Budheswar Dehury]

Dear GROMACS Developers and users,

While trying to clustering analysis based on certain distance matrices, 
however, while trying to perform PCA, I executed the following command, it 
shows the following error. Need your valuable suggestion and feedback to get 
rid of such errors.

Thanking you
Budheswar

gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc
  :-) GROMACS - gmx covar, 2019.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. Berendsen
Par Bjelkmar  Christian Blau   Viacheslav Bolnykh Kevin Boyd
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Alan Gray
  Gerrit Groenhof Anca HamuraruVincent Hindriksen  M. Eric Irrgang
  Aleksei Iupinov   Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund
Pascal Merz Pieter MeulenhoffTeemu Murtola   Szilard Pall
Sander Pronk  Roland Schulz  Michael ShirtsAlexey Shvetsov
   Alfons Sijbers Peter Tieleman  Jon Vincent  Teemu 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) 2001-2018, 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 covar, version 2019.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/bd422/Desktop/BD/1
Command line:
  gmx covar -f pca.xtc -s pca_dummy.pdb -nofit -nomwa -nopbc


WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.


Choose a group for the covariance analysis
Group 0 ( System) has 66506 elements
Group 1 (Protein) has 66506 elements
Group 2 (  Protein-H) has 66506 elements
Group 3 (C-alpha) has 66506 elements
Group 4 (   Backbone) has 66506 elements
Group 5 (  MainChain) has 66506 elements
Group 6 (   MainChain+Cb) has 66506 elements
Group 7 (MainChain+H) has 66506 elements
Group 8 (  SideChain) has 0 elements
Group 9 (SideChain-H) has 0 elements
Select a group: 0
Selected 0: 'System'

---
Program: gmx covar, version 2019.2
Source file: src/gromacs/utility/smalloc.cpp (line 125)

Fatal error:
Not enough memory. Failed to calloc 39807432324 elements of size 4 for mat
(called from file
/home/bd422/Downloads/gromacs-2019.2/src/gromacs/gmxana/gmx_covar.cpp, line
260)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

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[gmx-users] gromacs pullcode

[zhaox]

Hi,There are two  groups in my system.When I use the pull code to pull one group along the axis X, setting pull_coord1_geometry =direction,I am confused with the "distance at start" and the "reference at t=0".Could anyone can tell me how to understand these?And if I use the absolute reference,how to understand these? For example,when I set the pull_coord1_origin=0 0 0,what means the "distance at start"?Thank you in advance.My pull code is followed:; Pull codefreezegrps          = bot    topfreezedim           = Y Y Y  N N  Npull                = yespull_ncoords        = 1           ; only one reaction coordinatepull_ngroups        = 2           ; one group defining one reaction coordinatepull_group1_name    = toppull_group2_name    = botpull_coord1_type    = constant-forcepull_coord1_geometry= direction;pull_coord1_origin  =pull_coord1_vec     = 1 0 0pull_coord1_groups  = 1 2pull_coord1_start   = yes;pull_coord1_rate    = -0.0001pull_coord1_dim     = y n npull_coord1_k       = 5000        ;KJ mol^-1 nm^-1  cos-acceleration    = 0.05pull_group1_pbcatom = 1384pull_group2_pbcatom = 554comm-mode            = linearnstcomm              = 10aomm-grps            =


 










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[gmx-users] gromacs pullcode

[zhaox]

Hi,There are two  groups in my system.When I use the pull code to pull one group along the axis X, setting pull_coord1_geometry =direction-periodic,I am confused with the "distance at start" and the "reference at t=0".Could anyone can tell me how to understand these?And if I use the absolute reference,how to understand these? For example,when I set the pull_coord1_origin=0 0 0，how to calculate “distance at start”？Thank you in advance.My pull code is followed:; Pull codefreezegrps          = bot    topfreezedim           = Y Y Y  n y npull                = yespull_ncoords        = 2           ; two reaction coordinates x and zpull_ngroups        = 2           ; one group defining one reaction coordinatepull_group1_name    = toppull_group2_name    = botpull_coord1_type    = umbrella    ;harmonic potentialpull_coord1_geometry= direction-periodicpull_coord1_vec     = 1 0 0pull_coord1_origin  = 0 0 0 pull_coord1_groups  = 0 1pull_coord1_start   = yespull_coord1_k       = 4000pull_coord1_rate    = 0.005pull_coord2_type    = constant-forcepull_coord2_geometry= distancepull_coord2_dim     = n n ypull_coord2_groups  = 1 2pull_coord2_start   = yespull_coord2_k       = 3838550        ;KJ mol^-1 nm^-1pull_group1_pbcatom  = 5806;pull_group2_pbcatom  = 1887pull-pbc-ref-prev-step-com = yescos-acceleration    = 0.05comm-mode            = linearnstcomm              = 10comm-grps            =                                     









 










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[gmx-users] Gromacs GPU

[tarzan p]

Hi all,I have started using GROMACS recently on my work station (2 X Intel 6148 
(20 cores each) and 2 x tesla v100 .I have compiled it as per the instructions 
atRun GROMACS 3X Faster on NVIDIA GPUs

I would like to get request for a proper benchmark for GPU version and would 
like to know how to run the GPU version. I mean the command to use one GPU and 
2 GPU(s).
With best wishes 

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[gmx-users] Gromacs tutorial

[Suprim Tha]

I was trying gromacs tutorial on molecular dynamics simulation of
protein-ligand complex. Everything was going well until the step to
convert CHARMM
jz4.str file into GROMACS files using the command
python cgenff_charmm2gmx_py2.py JZ4 jz4.mol2 jz4.str charmm36-mar2019.ff
The error was:
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (22) and
top (0) are unequal
Usually this means the specified residue name does not match between str
and mol2 files.
I have attached the generated str and mol2 files.
Please help me find the error.
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[gmx-users] gromacs Query

[Aman Deep]

sir is there any way to create only XTC file from mdrun only. the server on
which I am working is not providing enough space and my trr file is too
much large.

thank you

-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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Re: [gmx-users] Gromacs

[saranya]

I have already done simulation for protein and drug interacted protein
complexes for 100ns. I just checked out the pressure of my system by using
gmx energy command, but the calculated pressure is quite altered (20,000
pressure bar).
Moreover, when I calculated the temperature of my system, the result was
zero. I am not able to understand the origin of this discrepancy. kindly
consider the above issue and please help me out.

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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Re: [gmx-users] Gromacs

[Justin Lemkul]

On 6/7/17 8:36 AM, saranya wrote:

I have already done simulation for protein and drug interacted protein
complexes for 100ns. I just checked out the pressure of my system by using
gmx energy command, but the calculated pressure is quite altered (20,000
pressure bar).
Moreover, when I calculated the temperature of my system, the result was
zero. I am not able to understand the origin of this discrepancy. kindly
consider the above issue and please help me out.



How are you calculating these properties?  Is this directly the output from gmx 
energy?  What were your .mdp settings?


-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] Gromacs

[saranya]

I have simulated the protein in water and protein with ligand for 100ns by
using GPU and the edr file was generated using -rerun command on
another system.I have just checked the pressure of my system by using
gmx energy
command, then i have selected pressure (group), but the calculated pressure
is quite altered (20,000 pressure bar). Moreover, when I calculated the
temperature of my system, the result was zero.
I have used below mdp file for the calculation
title   = Protein-ligand complex NPT equilibration
define  = -DPOSRES_LIG  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 100 ps
nstvout = 100   ; save velocities every 100 ps
nstenergy   = 100   ; save energies every 100 ps
nstlog  = 100   ; update log file every 100 ps
energygrps  = Protein
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_EPI Water_and_ions; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; velocity generation off after NVT

*With Regards,*

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*
*Coimbatore-46*
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Re: [gmx-users] Gromacs

[Justin Lemkul]

On 6/8/17 3:10 AM, saranya wrote:

I have simulated the protein in water and protein with ligand for 100ns by
using GPU and the edr file was generated using -rerun command on
another system.I have just checked the pressure of my system by using
gmx energy
command, then i have selected pressure (group), but the calculated pressure
is quite altered (20,000 pressure bar). Moreover, when I calculated the
temperature of my system, the result was zero.


If you're recalculating energies from an .xtc, this is what you should expect. 
There are no velocities in an .xtc file so all properties related to kinetic 
energy (temperature and virial, hence pressure) are all garbage.


The original .edr file has these quantities.  You just can't use energygrps to 
decompose short-range nonbonded interaction energies on a GPU.  The other 
quantities are valid.


-Justin


I have used below mdp file for the calculation
title   = Protein-ligand complex NPT equilibration
define  = -DPOSRES_LIG  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 100 ps
nstvout = 100   ; save velocities every 100 ps
nstenergy   = 100   ; save energies every 100 ps
nstlog  = 100   ; update log file every 100 ps
energygrps  = Protein
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_EPI Water_and_ions; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; velocity generation off after NVT

*With Regards,*

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*
*Coimbatore-46*



--
==

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] Gromacs enquiry

[Odame Agyapong]

My name is Odame and I am currently working on a project that requires
molecular dynamics. I plan using GROMACS for my simulations.
Specifically I would like to simulate a membrane protein in POPC, TFE,
DPC and DHPC lipid layers.

First, how do I build or obtain these lipid bilayers. Is there a
software or online resource I can go to obtain them or gromacs package
provides these lipids?

Initially i tried a POPC simulation in GROMACS and was getting errors
in topology outputs. I was therefore unable to continue to the next
steps .Is there a tutorial specifically for simulating in these
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[gmx-users] gromacs error

[Neha Gupta]

Hi gromacs users,

How to fix this error?

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

PATH=$PATH:"/usr/local/gromacs/bin/"

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/local/gromacs/share/gromacs/top"



Thanks,
Neha
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[gmx-users] gromacs installation

[vijayakumar gosu]

Hi,

I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus.
I am allotted to use only 2 nodes with 80 cpus. after installation when i
did sample md run only 20 cpus are being utilized. How can I fully utilize
the all 80 CPUs for mdrun.

I have used below cmake command for the installation

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF
-DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs

I have not seen any errors during installation.

Thanks.
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[gmx-users] gromacs error

[Vidya R]

Hi,


When I give these two commands

gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min

I get this error.

What to do?



Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)

Thanks,
Vidya.R
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[gmx-users] gromacs-error.docx

[Vidya R (via Google Drive)]

I've shared an item with you:

gromacs-error.docx
https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU/view?usp=sharing&ts=59be86ad

It's not an attachment -- it's stored online. To open this item, just click  
the link above.

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[gmx-users] gromacs error

[Rahma Dahmani]

Hi,
How can i rectify the following GROMACS error?
Fatal error:
atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms
while sorting atoms.

Thank you for your help
-- 






*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*
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[gmx-users] Gromacs 5.1.4

[Chetan Puri]

I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40
But on the make step I am getting error
nvcc fatal : unsupported gpu architecture 'compute_20'
So can anyone suggest how to resolve it.
CHETAN
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[gmx-users] Gromacs error

[Kunal Dutta]

Hi,
I have the following problems

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON

CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):

  The GROMACS build will download FFTW 3.3.3 as requested, but it will not

  know the file it receives is correct.  If you now use



  make



   GROMACS will build and link to FFTW anyway, but there is a possible
security risk if you execute a GROMACS tool that calls this library.
Instead, you can use



  make fftwBuild



   to do just the download and build of FFTW, and then run



  md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz



  to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2.  If so, everything

  is OK and you should use



  make



   to proceed with the rest of the GROMACS build. Alternatively, you could
stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation
instructions to build FFTW yourself.





-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2

-- Configuring done

-- Generating done

-- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build

kunal@kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make

[  1%] Built target fftwBuild

[  1%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o

/usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
void*, size_t)’:

/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope

   return (char *) memcpy (__dest, __src, __n) + __n;

  ^

CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:264 (message):

  Error generating file


/home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o





src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383:
recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o'
failed

make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1

CMakeFiles/Makefile2:1609: recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed

make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2

Makefile:147: recipe for target 'all' failed

make: *** [all] Error 2
-- 
-
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933

ORCID ID: -0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284J&hl=en

-- 





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[gmx-users] Gromacs 2020

[Turega, Simon]

Hi all

After attempting to install GROMACS 2020 on new system, I get the error below. 
The system details &  other details are below the error.

 cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=gcc -DGMX_GPU=ON -Wno-dev

make

[ 84%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o
In file included from 
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:48:0,
 from 
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h: In 
instantiation of 'std::unique_ptr 
gmx::SimulatorBuilder::build(bool, Args&& ...) [with Args = {_IO_FILE*&, 
t_commrec*&, gmx_multisim_t*&, gmx::MDLogger&, int, const t_filenm*, 
gmx_output_env_t*&, gmx::MdrunOptions&, gmx::StartingBehavior&, gmx_vsite_t*, 
gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, gmx::IMDOutputProvider*, 
const gmx::MdModulesNotifier&, t_inputrec*&, gmx::ImdSession*, pull_t*&, 
t_swap*&, gmx_mtop_t*, t_fcdata*&, t_state*, ObservablesHistory*, 
gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*&, t_forcerec*&, gmx_enerdata_t*, 
gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, ReplicaExchangeParameters&, 
gmx_membed_t*&, gmx_walltime_accounting*&, 
std::unique_ptr >, const bool&}]':
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:1612:77:   
required from here
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h:94:23: 
error: use of deleted function 'std::unique_ptr<_Tp, _Dp>::unique_ptr(const 
std::unique_ptr<_Tp, _Dp>&) [with _Tp = gmx::StopHandlerBuilder; _Dp = 
std::default_delete]'
 using ISimulator::ISimulator;
   ^~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
 from 
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.h:48,
 from 
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:46:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: 
declared here
   unique_ptr(const unique_ptr&) = delete;
   ^~
In file included from 
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:0:
/home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:123:45: 
note: synthesized method 'gmx::LegacySimulator::LegacySimulator(FILE*, 
t_commrec*, const gmx_multisim_t*, const gmx::MDLogger&, int, const t_filenm*, 
const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior, 
gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*, 
gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*, 
gmx::ImdSession*, pull_t*, t_swap*, gmx_mtop_t*, t_fcdata*, t_state*, 
ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*, t_forcerec*, 
gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*, const 
ReplicaExchangeParameters&, gmx_membed_t*, gmx_walltime_accounting*, 
std::unique_ptr, bool)' first required here
 return std::unique_ptr(new 
LegacySimulator(std::forward(args)...));
 
^~~~
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

System details

Architecture: x86_64
CPU op modes: 32-bit, 64-bit

OS details

CentOS Linux release 7.3.1611 (Core)
Linux 3.10.0-327.22.2.el7.x86_64

Compiler/ nvcc details

openmpi/intel-ofed/gcc/64/1.10.4
Cuda 90 toolkit/9.0.176
gcc version 6.1.0

Thanks in advance for your help

Simon Turega
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[gmx-users] GROMACS automation

[Mohamed Abdelaal]

Hello everybody,

I am trying to insert molecules into a box but I have to insert one single
molecule at a time reaching 3000 molecule in total. Is there a way to
automate this process ?

Thanks
Mohamed
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Re: [gmx-users] gromacs

[Pavan Kumar]

Set the installed path and library path of Gromacs in .bashrc file and
source it


On Tue, Apr 1, 2014 at 1:36 PM, Meenakshi Rajput wrote:

> i used the pdb2gmx command but i get a message "command not found". can you
> help me
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Thanks & Regards,
Pavan Kumar
Project Engineer
CDAC -KP
Ph +91-7676367646
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Re: [gmx-users] gromacs

[Jernej Zidar]

Please please read the basics (i.e. how to use) about Gromacs before
posting questions.
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[gmx-users] gromacs 5.0

[gejingming]

dear sir,
now ,I am using gromacs 5.0 VERSION ,but there is not g_membed and tpbconv 
commond.I think it is important for us.can you add these commond to the new 
version.
   thank you!
gjm
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[gmx-users] Gromacs with InflateGro

[Nash, Anthony]

Hi all,

I'm really struggling to get InflateGro to work in a dimer + lipid (no water or 
ions) system. The fault seems to happen when the regular expression to break 
the .gro entry reads in an entry from C  to C1. I managed to generalise 
the regex further and now using substr to explicitly pull out the entries I 
want. Unfortunately I'm a little confused as to the purpose of a variable 
called 'now'.  Has anyone got a bullet proof copy of the code working with 
+ atoms as I've had enough going through this file.

I also tried InflateGro2, which passes the first two iterations but then dies 
after the second. It can't find tmp_out.gro, as the previous entry hadn't 
successfully passed grompp due to a difference in atom count between .gro and 
.top. 


Thanks
Anthony 
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[gmx-users] GROMACS 5.0.5 released

[Mark Abraham]

Hi Gromacs users,

The official release of Gromacs 5.0.5 is available! It contains several
fixes to mdrun and analysis tools. Please see the link to the release notes
below for more details. There are also some minor performance enhancements,
warnings and documentation fixes. We encourage all users to upgrade their
installations from earlier 5.0 releases.

You can find the code, manual, release notes, installation instructions and
test suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.5.tar.gz

ftp://ftp.gromacs.org/pub/manual/manual-5.0.5.pdf

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0.5

http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0

http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz

Happy simulating!

Mark Abraham
Gromacs development manager
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[gmx-users] Gromacs in UBUNTU

[saeed poorasad]

Dear Gromacs users ,
Greetings .I want to install Gromacs with using of UBUNTU software center .  
Now I want to know about updating process of this version of gromacs . Does it 
update automatically with Ubuntu ? 
Thanks for your attention .Best,Saeed.  
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Re: [gmx-users] Gromacs Error

[Tsjerk Wassenaar]

Hi Manoj,

The error is clear. Check the settings referred to in your .mdp file and
modify them accordingly.

Cheers,

Tsjerk
On May 19, 2015 07:35, "manoj damale" 
wrote:

> Dear All,
> i'm geting below error while subjecting my system (Protein-ligand) for
> equlibriation in nvt.mdp file
>
> mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro
> -p topol.top -n index.ndx -o nvt.tpr
>  :-)  G  R  O  M  A  C  S  (-:
>
>GRowing Old MAkes el Chrono Sweat
>
> :-)  VERSION 4.5.3  (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>Berk Hess, David van der Spoel, and Erik Lindahl.
>
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
> :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -fnvt.mdp  Inputgrompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c em.gro  InputStructure file: gro g96 pdb tpr etc.
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>   -n  index.ndx  Input, Opt!  Index file
>   -p  topol.top  InputTopology file
>  -pp  processed.top  Output, Opt. Topology file
>   -onvt.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint0   Set the nicelevel
> -[no]v   bool   no  Be loud and noisy
> -timereal   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with
> virtual
> sites
> -maxwarn int0   Number of allowed warnings during input
> processing
> -[no]zerobool   no  Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
> atomtypes
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
>
> ERROR 1 [file nvt.mdp]:
>   With coulombtype = PME-Switch, rcoulomb must be <= rlist
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'UNT'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
> Setting gen_seed to 3507
> Velocities were taken from a Maxwell distribution at 300 K
>
> ---
> Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1356
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "Yeah, a Wuzz, Or a Jerk" (F. Black)
>  With Best Regards.
>
> Mr.Manoj Damale,
> M.S. Pharma (Pharmacoinformatics) NIPER,
> Kolkata, West Bengal State,
> India.
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> posting!
>
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>
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Re: [gmx-users] Gromacs Error

[Tsjerk Wassenaar]

ERROR 1 [file nvt.mdp]:
  With coulombtype = PME-Switch, rcoulomb must be <= rlist

On Tue, May 19, 2015 at 10:25 AM, manoj damale <
manojaurangabad...@yahoo.co.in> wrote:

> what exactly i should modify
>
> With Best Regards.
>
>
> Mr.Manoj Damale,
> M.S. Pharma (Pharmacoinformatics) NIPER,
> Kolkata, West Bengal State,
> India.
>
>
>
>   On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar 
> wrote:
>
>
> Hi Manoj,
> The error is clear. Check the settings referred to in your .mdp file and
> modify them accordingly.
> Cheers,
> Tsjerk
> On May 19, 2015 07:35, "manoj damale" 
> wrote:
>
> Dear All,
> i'm geting below error while subjecting my system (Protein-ligand) for
> equlibriation in nvt.mdp file
>
> mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro
> -p topol.top -n index.ndx -o nvt.tpr
>  :-)  G  R  O  M  A  C  S  (-:
>
>GRowing Old MAkes el Chrono Sweat
>
> :-)  VERSION 4.5.3  (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>Berk Hess, David van der Spoel, and Erik Lindahl.
>
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
> :-)  grompp  (-:
>
> Option Filename  Type Description
> 
>   -fnvt.mdp  Inputgrompp input file with MD parameters
>  -po  mdout.mdp  Output   grompp input file with MD parameters
>   -c em.gro  InputStructure file: gro g96 pdb tpr etc.
>   -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>  -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>   -n  index.ndx  Input, Opt!  Index file
>   -p  topol.top  InputTopology file
>  -pp  processed.top  Output, Opt. Topology file
>   -onvt.tpr  Output   Run input file: tpr tpb tpa
>   -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e   ener.edr  Input, Opt.  Energy file
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint0   Set the nicelevel
> -[no]v   bool   no  Be loud and noisy
> -timereal   -1  Take frame at or first after this time.
> -[no]rmvsbds bool   yes Remove constant bonded interactions with
> virtual
> sites
> -maxwarn int0   Number of allowed warnings during input
> processing
> -[no]zerobool   no  Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum   bool   yes Renumber atomtypes and minimize number of
> atomtypes
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.18#
>
> ERROR 1 [file nvt.mdp]:
>   With coulombtype = PME-Switch, rcoulomb must be <= rlist
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'UNT'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
> Setting gen_seed to 3507
> Velocities were taken from a Maxwell distribution at 300 K
>
> ---
> Program grompp, VERSION 4.5.3
> Source code file: grompp.c, line: 1356
>
> Fatal error:
> There was 1 error in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "Yeah, a Wuzz, Or a Jerk" (F. Black)
>  With Best Regards.
>
> Mr.Manoj Damale,
> M.S. Pharma (Pharmacoinformatics) NIPER,
> Kolkata, West Bengal State,
> India.
> --
> Gromacs Use

[gmx-users] GROMACS http download?

[Jorge Fernandez de Cossio Diaz]

I can't access the tar.gz at http://www.gromacs.org/Downloads because it is on 
FTP, which my (corporate) proxy blocks.

Is there an http mirror where I can download these files? I need to download 
these:
ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.5.tar.gz
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz

Thanks in advance.
---

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[gmx-users] gromacs-loacal pressure

[Soheila Aghdam]

dera all
I need to rerun mysimulation with modified gromacs package for computing
local pressure
but I couldnt install modified gromacs package
this is the error:
make[3]: Entering directory
`/home/soheila/program/gromacs-4.0.2_localpressure/src'
make[3]: Leaving directory
`/home/soheila/program/gromacs-4.0.2_localpressure/src'
make[2]: Leaving directory
`/home/soheila/program/gromacs-4.0.2_localpressure/src'
make[1]: Leaving directory
`/home/soheila/program/gromacs-4.0.2_localpressure/src'
...and more

and I couldnt find the commands for using this type of gromacs,is there any
refrence for localpressure commands?or i think i have to add "LP" after
original commands

thank you so much
Soheila
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[gmx-users] GROMACS ftp server

[Mark Abraham]

Hi,

We've had some issues with availability of the ftp server that hosts some
of the GROMACS, so I have moved the content to temporary hosting. Links
from
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[gmx-users] GROMACS ftp server

[Mark Abraham]

Hi,

Sorry for the misclick in my previous post. We've had some issues with
availability of the ftp server that hosts some of the GROMACS content, so I
have moved it to another location. Links from
http://www.gromacs.org/Downloads to the most recent tarballs now work, but
not all will work yet. Please let me know if there's a specific need not
met.

Mark
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[gmx-users] gromacs gpu code

[Wayne Liang]

Dear developers,

I would like to write a new gromacs tool which can make use of GPU. I
have some experience for implementing new analysis tools since gmx3.3
(but only for cpu). I plan to write a cuda kernel that can be called
from standard c code (g_xxx.c).

I was trying to dig into nbnxn_cuda folder to find some hints of compiling
cuda and c codes together. However, the CMakeList.txt makes me a bit
confused.

I would like to know is there any templates (CMakeList) I can refer
to? or any other source that i can learn from? Thanks for all the
suggestions.


Best,

Chungwen
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[gmx-users] GROMACS wall parameters

[shivangi nangia]

Hello All,

Is there any tutorial/example of how to apply wall potential in GROMACS.

I basically want to design a system where there are two walls just above
and below the head groups of a bilayer, so that I am able to restrain an
inserted peptide from popping out to the surface or in water.

http://manual.gromacs.org/online/mdp_opt.html#walls


Thi link says:

a) I can apply 2 walls, one being at z=0 and the other at z=z-box

here "box" means the length of the box in z-direction?

b) *wall-atomtype:*
the atom type name in the force field for each wall. By (for example)
defining a special wall atom type in the topology with its own combination
rules, this allows for independent tuning of the interaction of each
atomtype with the walls.
Is there a way that I can specify that the "head-groups" in the .itp file
as wall-atomtype?

Kindly guide.

Thanks,sxn
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[gmx-users] GROMACS 5.0.6 released

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 5.0.6 is available! It contains quite a few
fixes to mdrun and analysis tools. In particular, we have fixed one
potentially serious bug with how 5.0 pdb2gmx interprets multiple
interactions on the same atoms in .rtp entries for some force fields.
Please see the link to the release notes below for more details. There are
also some new warnings and documentation fixes. We encourage all users to
upgrade their installations from earlier 5.0 releases.

You can find the code, manual, release notes, installation instructions and
test suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.6.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-5.0.6.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0.6
http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
http://gerrit.gromacs.org/download/regressiontests-5.0.6.tar.gz

Happy simulating!

Mark Abraham
GROMACS development manager
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Re: [gmx-users] Gromacs Path

[James Lord]

Hi Vikas,
 typing mdrun or which mdrun in your terminal will tell you where it is
installed.
Cheers
James

On Monday, July 27, 2015, Live King  wrote:

> Hi Everyone,
>
> I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs,
> then what is path of my Gromacs directory ? I don't seem to find it
> anywhere .
>
> Thanks,
> vikas
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[gmx-users] gromacs 5.0.5 install

[신은혜]

I installed gromacs 5.0.5, but during installation, i got error massages
 
CMake Error at src/programs/cmake_install.cmake:42 (FILE):
  file INSTALL cannot find
  "//phome01/p580seh/gromacs-5.0.5/build/bin/gmx_mpi_d".
Call Stack (most recent call first):
  src/cmake_install.cmake:40 (INCLUDE)
  cmake_install.cmake:48 (INCLUDE)

make: *** [install] Error 1 
 
I also check this option : -DGMX_MPI=on
 
how to fix it ?
 
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[gmx-users] Gromacs and Gcc5.2

[Nicolas Cheron]

Dear all,

I am wondering if there is an official statement regarding compiling
Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended
or not? Should we expect improvements? I have tried quickly some small
benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on
ns/day between 1 and 3% (with respect to gcc4.8.5).

Also, during compilation I get several warnings such as:

In file included from /usr/local/openmpi-gnu/include/mpi.h:253:0,
 from
/home2/ncheron/Programs/gromacs-5.1/src/gromacs/utility/gmxmpi.h:59,
 from
/home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/types/commrec.h:45,
 from
/home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/gmx_ga2la.h:40,
 from
/home2/ncheron/Programs/gromacs-5.1/src/gromacs/domdec/domdec_constraints.cpp:55:
/usr/local/openmpi-gnu/include/mpi_portable_platform.h:374:34: warning:
invalid suffix on literal; C++11 requires a space between literal and
string macro [-Wliteral-suffix]

_STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__)

I don't think it is relevant and I am not worried about it, but just wanted
to check with you.

Thank you.

Nicolas
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[gmx-users] GROMACS On GPU

[Nikhil Maroli]

I have workstation with Tesla K20 GPU and Ubuntu 14.04 OS
if i just give sudo apt-get install gromacs it will work with GPU or should
do something else?
thanks in advance

-- 
Ragards,
Nikhil Maroli
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[gmx-users] GROMACS 5.0.7 released

[Mark Abraham]

Hi GROMACS users,

The official release of GROMACS 5.0.7 is available! It contains a few fixes
to mdrun (which are either minor in consequence or rare in occurrence), and
analysis tools. Please see the link to the release notes below for more
details. There are also some new warnings and documentation fixes. We
encourage all users to upgrade their installations from earlier 5.0
releases.

This is the last planned release in the 5.0 series. We will only make a
release of 5.0.8 if a serious issue of scientific correctness is identified
and fixed. Naturally, we will continue to make regular bug-fix releases in
the 5.1 series.

You can find the code, manual, release notes, installation instructions and
test suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.7.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x/v5.0.7
http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
http://gerrit.gromacs.org/download/regressiontests-5.0.7.tar.gz

Happy simulating!

Mark Abraham
GROMACS development manager
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[gmx-users] gromacs openmpi error

[????]

Hi everyone,

   I want to install gromacs in the GPU, I have installed  

fftw-3.3.tar.gz   openmpi-1.6.5cmake-3.0  gromacs-4.6.5.tar.gz

if I use several nodes, it appears error 

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

How to solve the problem?

Thank you in advance
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Re: [gmx-users] gromacs error

[Smith, Micholas D.]

Check your topology file (.top) and make sure you have ions.itp imported and 
that you are using the proper naming convention of sodium for your force-field.

Hope that helps.

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Puneet 

Sent: Wednesday, December 09, 2015 7:33 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs error

Hello



I am doing Protein-Ligand simulation and I face following error while
running command "grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o
em.tpr". Kindly assist me how can I rectify error ?



Error



Program grompp, version 3.3.3

source code file: toppush.c, line: 1396



Fatal error:

No such moleculetype NA



Please reply as soon as possible its really urgent for me.



Regards

Puneet Kaur



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[gmx-users] Gromacs Workshop 2016?

[Deva Priya]

Hello,

I was wondering if a summer workshop is being planned in US, and if any
tentative plans are in place.

Thanks,
Deva
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Re: [gmx-users] Gromacs Tutorial

[XAvier Periole]

Bastards … 

On Jan 19, 2016, at 2:00 PM, Tsjerk Wassenaar  wrote:

> Hey :)
> 
> As some of you know, some years ago I developed an extensive Gromacs
> tutorial (at the University of Utrecht). That work has caught they eye of
> educators, and now the tutorial is published as an educational paper! Just
> kind of funny that I'm not an author.
> For those interested:
> 
> http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
> 
> Enjoy!
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Gromacs Tutorial

[Simone Bolognini]

Just crazy!!! Aren't you going to do something about it??
Il 19/gen/2016 23:11, "XAvier Periole"  ha scritto:

>
> Bastards …
>
> On Jan 19, 2016, at 2:00 PM, Tsjerk Wassenaar  wrote:
>
> > Hey :)
> >
> > As some of you know, some years ago I developed an extensive Gromacs
> > tutorial (at the University of Utrecht). That work has caught they eye of
> > educators, and now the tutorial is published as an educational paper!
> Just
> > kind of funny that I'm not an author.
> > For those interested:
> >
> > http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
> >
> > Enjoy!
> >
> > Tsjerk
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gromacs Tutorial

[Peter Stern]

The only thing that you can do about this is to learn from the experience and 
in the future, copyright everything that you create and distribute.  Then 
nobody can "plagiarize" your work without your permission.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Tuesday, January 19, 2016 3:01 PM
To: mdgroup; Discussion list for GROMACS users
Subject: [gmx-users] Gromacs Tutorial

Hey :)

As some of you know, some years ago I developed an extensive Gromacs tutorial 
(at the University of Utrecht). That work has caught they eye of educators, and 
now the tutorial is published as an educational paper! Just kind of funny that 
I'm not an author.
For those interested:

http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract

Enjoy!

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Gromacs Tutorial

[João Henriques]

Well... he did get acknowledged :) Plus, I doubt anyone here besides Tsjerk
and his old colleagues knows who "legally" has the right to his work. What
I mean is that, for example, in my current institution, the student has the
right to products of his/her labour, but in other countries the institution
and/or the research group owns it, and so they can do as they please with
it (more or less, but you get the point).

Anyway, thanks for the link, this article will go straight into the hands
of my new master's student, who is just starting in this field of research.

Best regards,
/J


On Wed, Jan 20, 2016 at 11:00 AM, Peter Stern 
wrote:

> The only thing that you can do about this is to learn from the experience
> and in the future, copyright everything that you create and distribute.
> Then nobody can "plagiarize" your work without your permission.
>
> Peter
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
> Wassenaar
> Sent: Tuesday, January 19, 2016 3:01 PM
> To: mdgroup; Discussion list for GROMACS users
> Subject: [gmx-users] Gromacs Tutorial
>
> Hey :)
>
> As some of you know, some years ago I developed an extensive Gromacs
> tutorial (at the University of Utrecht). That work has caught they eye of
> educators, and now the tutorial is published as an educational paper! Just
> kind of funny that I'm not an author.
> For those interested:
>
> http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
>
> Enjoy!
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> 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.
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Re: [gmx-users] Gromacs Tutorial

[Tsjerk Wassenaar]

Hey Guys,

I did not mean to make this a scandal of some sort! If you think anything
of it like that, please contact me directly.

The paper is interesting! That's a reason to share it.

I also need to note (now certainly) that the paper does not discuss the
didactical issues and considerations that made my tutorial the way it was,
but the paper addresses the changes the group made to it afterwards. I
would have loved to be part of that, and I think it would have been nice to
add my few cents on the underlying principles which are still at the core
of the tutorial. But this is the tutorial it is now, and that's the work of
Joao, Adrien and Alexandre (who are dear to me).

Joao (Henriques) hits the nail: Interesting paper/tutorial, Work of the
Insitute, they acknowledged me.

Case closed. Read the paper, tell your students.

Cheers,

Tsjerk



On Wed, Jan 20, 2016 at 11:45 AM, João Henriques <
joao.henriques.32...@gmail.com> wrote:

> Well... he did get acknowledged :) Plus, I doubt anyone here besides Tsjerk
> and his old colleagues knows who "legally" has the right to his work. What
> I mean is that, for example, in my current institution, the student has the
> right to products of his/her labour, but in other countries the institution
> and/or the research group owns it, and so they can do as they please with
> it (more or less, but you get the point).
>
> Anyway, thanks for the link, this article will go straight into the hands
> of my new master's student, who is just starting in this field of research.
>
> Best regards,
> /J
>
>
> On Wed, Jan 20, 2016 at 11:00 AM, Peter Stern 
> wrote:
>
> > The only thing that you can do about this is to learn from the experience
> > and in the future, copyright everything that you create and distribute.
> > Then nobody can "plagiarize" your work without your permission.
> >
> > Peter
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
> > Wassenaar
> > Sent: Tuesday, January 19, 2016 3:01 PM
> > To: mdgroup; Discussion list for GROMACS users
> > Subject: [gmx-users] Gromacs Tutorial
> >
> > Hey :)
> >
> > As some of you know, some years ago I developed an extensive Gromacs
> > tutorial (at the University of Utrecht). That work has caught they eye of
> > educators, and now the tutorial is published as an educational paper!
> Just
> > kind of funny that I'm not an author.
> > For those interested:
> >
> > http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
> >
> > Enjoy!
> >
> > Tsjerk
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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.
> > --
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> >
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] gromacs error

[Mehreen Jan]

how to run gromacs for protein protein interaction having phosphorylated at SER 
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields

>make changes in .rtp file
make changes in .dat file
forcefield 43A1 is used.

command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
error:
residue "TPO" not found in residue topology database

make changes in residuestypes.dat
fallowing are the changes make in .rtp file

; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms


[ SEP ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 2
   OGOA-0.36000 2
P P 0.94000 2
  O1POP-0.86000 2
  O2POP-0.86000 2
  O3POP-0.86000 2
C C   0.380 3
O O  -0.380 3
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CBOGgb_17   
   OG Pgb_27   
P   O1Pgb_23   
P   O2Pgb_23   
P   O3Pgb_23   
[ angles ]
;  aiajak   gromos type
   -C N H ga_31   
H NCA ga_17   
   -C NCA ga_30   
NCA C ga_12   
   CA C+N ga_18   
   CA C O ga_29   
O C+N ga_32   
NCACB ga_12   
CCACB ga_12   
   CACBOG ga_12   
   CBOG P ga_25
   OG P   O1P ga_13
   OG P   O2P ga_13
   OG P   O3P ga_13
  O1P P   O2P ga_28
  O1P P   O3P ga_28
  O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1   
CCA+N O gi_1   
   CA N CCB gi_2   
[ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_4   
   -C NCA C gd_19   
NCA C+N gd_20   
NCACBOG gd_17   
   CACBOG P gd_14   
   CBOG P   O1P gd_11

[ TPO ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH1 0.0 2
  OG1OA-0.36000 2
P P 0.94000 2
  O1POP-0.86000 2
  O2POP-0.86000 2
  O3POP-0.86000 2
  CG2   CH3 0.0 3
C C   0.380 4
O O  -0.380 4
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CB   OG1gb_17   
   CB   CG2gb_26   
  OG1 Pgb_27   
P   O1Pgb_23   
P   O2Pgb_23   
P   O3Pgb_23   
[ angles ]
;  aiajak   gromos type
   -C N H ga_31   
H NCA ga_17   
   -C NCA ga_30   
NCA C ga_12   
   CA C+N ga_18   
   CA C O ga_29   
O C+N ga_32   
NCACB ga_12   
CCACB ga_12   
   CACB   OG1 ga_12   
   CACB   CG2 ga_14   
  OG1CB   CG2 ga_14   
   CB   OG1 P ga_25
  OG1 P   O1P ga_13
  OG1 P   O2P ga_13
  OG1 P   O3P ga_13
  O1P P   O2P ga_28
  O1P P   O3P ga_28
  O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
N-CCA H gi_1   
CCA+N O gi_1   
   CA N CCB gi_2   
   CB   OG1   CG2CA gi_2   
[ dihedrals ]
;  aiajakal   gromos type
  -CA-C NCA gd_4   
   -C NCA C gd_19   
NCA C+N gd_20   
NCACB   OG1 gd_17   
   CACB   OG1 P gd_14   
   CB   OG1 P   O1P gd_11

[ PTR ]
[ atoms ]
N N-0.28000 0
H H 0.28000 0
   CA   CH1 0.0 1
   CB   CH2 0.0 1
   CG C 0.0 1
  CD1 C-0.1 2
  HD1HC 0.1 2
  CD2 C-0.1 3
  HD2HC 0.1 3
  CE1 C-0.1 4
  HE1HC 0.1 4
  CE2 C-0.1 5
  HE2HC 0.1 5
   CZ C 0.0 6
   OHOA-0.36000 6
P P 0.94000 6
  O1POP-0.86000 6
  O2POP-0.86000 6
  O3POP-0.86000 6
C C   0.380 7
O O  -0.380 7
[ bonds ]
N Hgb_2   
NCAgb_20   
   CA Cgb_26   
C Ogb_4   
C+Ngb_9   
   CACBgb_26   
   CBCGgb_26   
   CG   CD1gb_15   
   CG   CD2gb_15   
  CD1   HD1gb_3   
  CD1   CE1gb_15   
  CD2   HD2gb_3   
  CD2   CE2gb_15   
  CE1   HE1gb_3   
  CE1CZgb_15   
  CE2   HE

Re: [gmx-users] gromacs error

[Justin Lemkul]

On 2/1/16 1:06 AM, Mehreen Jan wrote:

how to run gromacs for protein protein interaction having phosphorylated at SER 
and THR.
error:
residue TPO not found in residue topology database
modification are done from the given web.
http://www.gromacs.org/Downloads/User_contributions/Force_fields


make changes in .rtp file

make changes in .dat file
forcefield 43A1 is used.

command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
error:
residue "TPO" not found in residue topology database



This means whatever either (1) you did not make the changes in the 
directory/file you thought or (2) you did not choose the right force field when 
prompted by pdb2gmx.  Without the full screen output from pdb2gmx, it's 
impossible to tell.


-Justin


make changes in residuestypes.dat
fallowing are the changes make in .rtp file

; [ SEP ] [ TPO ] [ PTR ] -PO4^{-2} forms
; [ SEPH ] [ TPOH ] [ PTRH ] -PO4H^{-1} forms


[ SEP ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH2 0.0 2
OGOA-0.36000 2
 P P 0.94000 2
   O1POP-0.86000 2
   O2POP-0.86000 2
   O3POP-0.86000 2
 C C   0.380 3
 O O  -0.380 3
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26
CBOGgb_17
OG Pgb_27
 P   O1Pgb_23
 P   O2Pgb_23
 P   O3Pgb_23
[ angles ]
;  aiajak   gromos type
-C N H ga_31
 H NCA ga_17
-C NCA ga_30
 NCA C ga_12
CA C+N ga_18
CA C O ga_29
 O C+N ga_32
 NCACB ga_12
 CCACB ga_12
CACBOG ga_12
CBOG P ga_25
OG P   O1P ga_13
OG P   O2P ga_13
OG P   O3P ga_13
   O1P P   O2P ga_28
   O1P P   O3P ga_28
   O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
 N-CCA H gi_1
 CCA+N O gi_1
CA N CCB gi_2
[ dihedrals ]
;  aiajakal   gromos type
   -CA-C NCA gd_4
-C NCA C gd_19
 NCA C+N gd_20
 NCACBOG gd_17
CACBOG P gd_14
CBOG P   O1P gd_11

[ TPO ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH1 0.0 2
   OG1OA-0.36000 2
 P P 0.94000 2
   O1POP-0.86000 2
   O2POP-0.86000 2
   O3POP-0.86000 2
   CG2   CH3 0.0 3
 C C   0.380 4
 O O  -0.380 4
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26
CB   OG1gb_17
CB   CG2gb_26
   OG1 Pgb_27
 P   O1Pgb_23
 P   O2Pgb_23
 P   O3Pgb_23
[ angles ]
;  aiajak   gromos type
-C N H ga_31
 H NCA ga_17
-C NCA ga_30
 NCA C ga_12
CA C+N ga_18
CA C O ga_29
 O C+N ga_32
 NCACB ga_12
 CCACB ga_12
CACB   OG1 ga_12
CACB   CG2 ga_14
   OG1CB   CG2 ga_14
CB   OG1 P ga_25
   OG1 P   O1P ga_13
   OG1 P   O2P ga_13
   OG1 P   O3P ga_13
   O1P P   O2P ga_28
   O1P P   O3P ga_28
   O2P P   O3P ga_28
[ impropers ]
;  aiajakal   gromos type
 N-CCA H gi_1
 CCA+N O gi_1
CA N CCB gi_2
CB   OG1   CG2CA gi_2
[ dihedrals ]
;  aiajakal   gromos type
   -CA-C NCA gd_4
-C NCA C gd_19
 NCA C+N gd_20
 NCACB   OG1 gd_17
CACB   OG1 P gd_14
CB   OG1 P   O1P gd_11

[ PTR ]
[ atoms ]
 N N-0.28000 0
 H H 0.28000 0
CA   CH1 0.0 1
CB   CH2 0.0 1
CG C 0.0 1
   CD1 C-0.1 2
   HD1HC 0.1 2
   CD2 C-0.1 3
   HD2HC 0.1 3
   CE1 C-0.1 4
   HE1HC 0.1 4
   CE2 C-0.1 5
   HE2HC 0.1 5
CZ C 0.0 6
OHOA-0.36000 6
 P P 0.94000 6
   O1POP-0.86000 6
   O2POP-0.86000 6
   O3POP-0.86000 6
 C C   0.380 7
 O O  -0.380 7
[ bonds ]
 N Hgb_2
 NCAgb_20
CA Cgb_26
 C Ogb_4
 C+Ngb_9
CACBgb_26

[gmx-users] Gromacs DFTB problem

[Gábor Balogh]

Dear Gromacs users,
I have compiled a DFTB implementation for GROMACS:
http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3

The system consists of the catalytic domain of a protein in explicit
solvent (TIP3P). Long-range electrostatics is calculated using the PME
scheme. Conjugate-gradient energy minimization runs fine, but NVT
equilibration terminates after 16-44 ps (depending on PME options and
velocity generation) with the following error message:

DSYGVD: ier = 214
EXITING!

MD options:

define  = -DPOSRES_SIM
;
integrator  = md
; 1 ns
nsteps  = 100
dt  = 0.001
; Output control
nstxout = 2
nstvout = 2
nstenergy   = 1
nstlog  = 2000
nstxtcout   = 1
xtc-grps= Protein
;
continuation= no
constraint_algorithm = lincs
constraints = all-bonds
;
ns_type = grid
nstlist = 10
rlist   = 1.0
rcoulomb= 1.0
rvdw= 1.0
;
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.12
;
tcoupl  = V-rescale
tc-grps = Protein_Link   Water_and_ions
tau_t   = 0.1   0.1
ref_t   = 310   310
;
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
;
DispCorr= EnerPres
;
gen_vel = yes
gen_temp= 310
gen_seed= -1
;
cutoff-scheme   = group
; dftb
QMMM= yes
QMMM-grps   = QMsystem  ; needs to be specified in the index file
QMMMscheme  = normal
QMmethod= RHF   ; required but ignored
QMbasis = STO-3G; required but ignored
QMcharge= -1; an integer
MMchargescalefactor = 1.; or smaller
; DFTB
QMdftbsccmode   = 3 ; for DFTB3, or 2 for DFTB2 (a.k.a. SCC-DFTB)
QMdftb-telec= 310.  ; "electronic temperature" for the Fermi
distribution
QMdftb-slko-path= /scratch1/BG/gro/slko_gmx/; path to the
parameter files including the trailing slash
QMdftb-slko-separator   =   ; possibly the character between element
names
QMdftb-slko-lowercase   = yes   ; or no, in the file names ("Ca"
vs. "ca")
QMdftb-slko-suffix  = -c.spl; of the file names
QMdftb-partial-pme  = 0 ; accelerated PME calculations -
recommended (0 to switch off)
QMdftb-dispersion   = 0 ; for D3, or 0 for no dispersion
QMdftb-cdko = 0 ; currently not implemented
QMdftb-mmhub-inf= 1 ; currently not implemented

Last lines of Gromacs-DFTB output:
STEP 24856


The number of MM atoms is 15355
MM+ETC   TIME: 24791883
EWALD-SR START
DFTB SR  TIME:  1860179
EWALD-SR END
DFTB PRE TIME:  2965810
SCC ITER TIME: 68803390
DFTB PME TIME:  4833495
DFTB DIA TIME: 12378935
SCC ITER TIME: 20096442
DFTB PME TIME:  4796196
DFTB DIA TIME: 12375332
SCC ITER TIME: 20050119
DFTB PME TIME:  4764749
DFTB DIA TIME: 12401352
SCC ITER TIME: 20061356
DFTB PME TIME:  4765373
DFTB DIA TIME:  7992655

DSYGVD: ier = 214
EXITING!

Could somebody help me to find out why the simulation is crashing?
Thanks in advance.

Best regards,
Gabor
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Re: [gmx-users] Gromacs Installation

[Justin Lemkul]

On 4/12/16 7:08 AM, ABANTIKA PAL wrote:

Hi,

I have installed GROMACS 5.1.2 by performing the steps described in the installation 
guide. All the steps have been executed successfully. But, no executable of mdrun is  
created in the build folder. Moreover, upon executing "which gromacs", its 
showing
  no gromacs in 
(/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
Please help how to resolve the issue.



The binary is called gmx.

-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] Gromacs Installation

[ABANTIKA PAL]

Thanks.

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, April 12, 2016 4:54:19 PM
Subject: Re: [gmx-users] Gromacs Installation



On 4/12/16 7:08 AM, ABANTIKA PAL wrote:
> Hi,
>
> I have installed GROMACS 5.1.2 by performing the steps described in the 
> installation guide. All the steps have been executed successfully. But, no 
> executable of mdrun is  created in the build folder. Moreover, upon executing 
> "which gromacs", its showing
>   no gromacs in 
> (/usr/local/gromacs/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/user1/.local/bin:/home/user1/bin
> Please help how to resolve the issue.
>

The binary is called gmx.

-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] gromacs fftw installation

[Neha Gandhi]

Dear List,

I am trying to install gromacs on a machine which is not allowed to connect
to the internet.
I have installed fftw in a directory /home/gandhin/fftw using --enable-float

I am trying to install gromacs but it always tries to download fftw and
therefore the installation ends up in error.

I am using following command
CMAKE_PREFIX_PATH=/home/gandhin/fftw-3.3.3/ cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=NONE
-DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx
-DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7

Any suggestion would be helpful.


-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Re: [gmx-users] Gromacs installation.

[Szilárd Páll]

With that amount of information it'll be hard for anyone to diagnose your
issue -- unless someone else ran into the same problem. If you want help
you need to i) try hard ii) try harder iii) describe what you tried and you
failed.

--
Szilárd

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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>
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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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