Re: [gmx-users] (no subject)

[Daniel Burns]

Start here: http://www.mdtutorials.com/gmx/.  An introduction to linux book
might be helpful as well if you are not already familiar with it.

Good luck!

On Thu, Apr 2, 2020 at 2:05 PM Feriel Terbeche  wrote:

> Hello!
> My name's FERIEL TERBECHE I am a genetic studant, from ALGERIA, Im
> preparing my  last study's project (master degrees), wich is about
> hemophila A and factor VIII where I have to use gromacs, but, I don't know
> how to use it even I have it on my computer and unfortunately no one here
> can help me because no one used it before.  I really need help but I don't
> know from where I'll get it, so can I have some advices. Thank you
>
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Re: [gmx-users] (no subject)

[Dallas Warren]

Download and use the forcefield files from the ATB server website, and then
make that you correctly point to it in your top file.

On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI,  wrote:

> Hi,
> I have been a new user and i was following the protein-ligand complex
> tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology
> i have used ATB webserver. I did download the .itp and .pdb file from there
> and converted that to .gro file. The problem i am facing is it shows an
> error while i add ions that "Atomtype CAro not found", although i have
> added the atomtypes in the gromacs topology file still it's showing the
> same error. I request if somebody could provie me a stepwise protocol i
> could follow.
>
> Thank you
>
> --
>
> Faisal Nabi
>
> *Pre-Doctoral Fellow (CSIR-JRF)*
> C/o Professor Rizwan Hassan Khan
> Interdisciplinary Biotechnology Unit,
> Aligarh Muslim University, Aligarh, UP, INDIA.
> Email-*fn...@myamy.ac.in *
> *  faisalbioc...@gmail.com *
> Contact no. - *+91-8923713214*
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Re: [gmx-users] no subject

[Prasanth G, Research Scholar]

Hello Faisal,

Easiest way to do this is by navigating to the MD files tab and download
the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This
molecule contains non-standard atom types not included in the standard
GROMOS 54A7 forcefield..."

The folder contains the procedure to modify the 54a7 forcefield to include
the non-standard atomtypes.
However the easiest way to just include the whole folder in your working
directory (wd) and when you prepare gro from pdb in the first step, you can
choose the option 1 (you will see that you receive a prompt saying this ff
is from the wd).
Hope it helps.

If you are interested in Ligand- protein interaction studies. I would
suggest you to use Amber or Charmm ff. This is because GROMOS is a united
atom ff and an all atom ff might be better in helping you understand these
interactions. Please go through the last part of this thread -
https://www.researchgate.net/post/How_can_I_use_a_Topology_file_generated_by_an_ATB_server

If you want to use Amber ff. you can use ACPYPE which works in conjunction
with AMBER to prepare files necessary in gromacs compatible format. As
antechamber (part of AMBER) is a semi qm/mm technique the parametrization
happens faster , plus it can be done directly on your system.

All the best



-- 
Regards,
Prasanth.
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Re: [gmx-users] (no subject)

[shakira shukoor]

Thanks christian for the detailed description.

On Mon, Feb 17, 2020 at 8:00 PM Christian Blau  wrote:

> Hi Shakkira,
>
>
> The simulation box deformation is described by six parameters that
> describe three basis box vectors with the following
> contraints,
>
>   - the first box vector is aligned along the x-axis, with coordinates
> thus has coordinates (xx,0,0)
>
>   - the second box vector is aligned in the x-y plane with coordinates
> (yx,yy,0)
>
>   - the third box vector is free (zx,zy,zz)
>
>
> The six parameters that you give in .mdp files are in the following order
>
> xx, yy, zz, yx, zx, zy
>
>
> The corrent box is then calculated as
>
> box(t_start)+(t-t_start)*deform
>
>
> For more information have a look at the gromacs manual mdp parameter
> description:
>
> http://manual.gromacs.org/current/user-guide/mdp-options.html
>
> under non-equilibrium MD:
>
> (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
> The velocities of deformation for the box elements: a(x) b(y) c(z)
> b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
> is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
> elements are corrected for periodicity. The coordinates are
> transformed accordingly. Frozen degrees of freedom are (purposely)
> also transformed. The time ts is set to t at the first step and at
> steps at which x and v are written to trajectory to ensure exact
> restarts. Deformation can be used together with semiisotropic or
> anisotropic pressure coupling when the appropriate
> compressibilities are set to zero. The diagonal elements can be
> used to strain a solid. The off-diagonal elements can be used to
> shear a solid or a liquid.
>
>
> Best,
>
> Christian
>
> On 2020-02-16 12:12, shakira shukoor wrote:
> >Hi all
> > Can anyone help me with the DEFORM option in Gromacs to change the box
> > values?
> >
> >
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-- 
*Best Regards*

Shakkira E
PhD student INSPIRE Scholar
Department of Chemistry
sdmdlab.xyz
IIT Patna
Bihta
Patna 801106
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Re: [gmx-users] (no subject)

[Christian Blau]

Hi Shakkira,


The simulation box deformation is described by six parameters that describe three basis box vectors with the following 
contraints,


 - the first box vector is aligned along the x-axis, with coordinates thus has 
coordinates (xx,0,0)

 - the second box vector is aligned in the x-y plane with coordinates (yx,yy,0)

 - the third box vector is free (zx,zy,zz)


The six parameters that you give in .mdp files are in the following order

xx, yy, zz, yx, zx, zy


The corrent box is then calculated as

box(t_start)+(t-t_start)*deform


For more information have a look at the gromacs manual mdp parameter 
description:

http://manual.gromacs.org/current/user-guide/mdp-options.html

under non-equilibrium MD:

   (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
   The velocities of deformation for the box elements: a(x) b(y) c(z)
   b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
   is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
   elements are corrected for periodicity. The coordinates are
   transformed accordingly. Frozen degrees of freedom are (purposely)
   also transformed. The time ts is set to t at the first step and at
   steps at which x and v are written to trajectory to ensure exact
   restarts. Deformation can be used together with semiisotropic or
   anisotropic pressure coupling when the appropriate
   compressibilities are set to zero. The diagonal elements can be
   used to strain a solid. The off-diagonal elements can be used to
   shear a solid or a liquid.


Best,

Christian

On 2020-02-16 12:12, shakira shukoor wrote:

   Hi all
Can anyone help me with the DEFORM option in Gromacs to change the box
values?



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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 2/14/20 12:05 AM, Neha Tiwari wrote:

Dear Gromacs experts,
I have generated topology files(.itp) of the ligand from the ATB server and
everything goes well, but when it comes to generating ions.tpr file, I am
getting following error.


$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

   :-) GROMACS - gmx grompp, 2018.1 (-:



 GROMACS is written by:

  Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C.
Berendsen

 Par BjelkmarAldert van Buuren   Rudi van Drunen Anton Feenstra

   Gerrit GroenhofAleksei Iupinov   Christoph Junghans   Anca Hamuraru

  Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus


   Carsten Kutzner  Per Larsson  Justin A. LemkulViveca Lindahl

   Magnus Lundborg   Pieter MeulenhoffErik Marklund  Teemu Murtola

 Szilard Pall   Sander Pronk  Roland Schulz Alexey Shvetsov

Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen

  Christian WennbergMaarten Wolf

and the project leaders:

 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2017, 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 grompp, version 2018.1

Executable:   /usr/bin/gmx

Data prefix:  /usr

Working dir:  /home/ya/Desktop/Neha/fecA/gromos

Command line:

   gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



NOTE 1 [file ions.mdp]:

   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

   that with the Verlet scheme, nstlist has no effect on the accuracy of

   your simulation.



Setting the LD random seed to 49113858

Generated 165 of the 1596 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein'

Excluding 3 bonded neighbours molecule type '4JCP'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 2 [file topol.top, line 45350]:

   System has non-zero total charge: -14.00

   Total charge should normally be an integer. See

   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

   for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet



ERROR 1 [file topol.top, line 45350]:

   atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 2 [file topol.top, line 45350]:

   atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 3 [file topol.top, line 45350]:

   atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 4 [file topol.top, line 45350]:

   atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 5 [file topol.top, line 45350]:

   atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 6 [file topol.top, line 45350]:

   atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 7 [file topol.top, line 45350]:

   atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 8 [file topol.top, line 45350]:

   atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 9 [file topol.top, line 45350]:

   atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 10 [file topol.top, line 45350]:

   atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 11 [file topol.top, line 45350]:

   atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 12 [file topol.top, line 45350]:

   atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 13 [file topol.top, line 45350]:

   atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 14 [file topol.top, line 45350]:

   atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







ERROR 15 [file topol.top, line 45350]:

   atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)







There were 2 notes



---

Program: gmx grompp, version 2018.1

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)



Fatal error:

There were 15 errors in input file(s)



Likely the format/contents of those topology lines are wrong if grompp 
finds zero mass.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

Re: [gmx-users] (no subject)

[Quyen V. Vu]

for what reasons you request the largest force in your system smaller than
such small value?

On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani  wrote:

> Dear Gromacs users
> I am running a free energy calculation of the protein-ligand complex.
> During the energy minimization process, I am getting many jumps in steps as
> below:-
>
> Step   Time
>   1050010500.0
>
>Energies (kJ/mol)
>Bond Restraint Pot.  AngleProper Dih.  Improper Dih.
> 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
> 6.81295e+037.12692e+043.37954e+05   -6.56537e+03   -2.70668e+06
>Coul. recip.Angle Rest. Dih. Rest.  Potential Pres. DC (bar)
> 4.78029e+035.32468e+003.32764e+00   -2.26802e+060.0e+00
>  Pressure (bar)dVremain/dl   dEkin/dl  dVcoul/dl   dVvdw/dl
>-2.69428e+040.0e+000.0e+002.78529e+03   -1.65404e+02
>  dVrestraint/dl   Constr. rmsd
> 0.0e+002.71623e-06
>
>Step   Time
>   1050110501.0
>
>Step   Time
>   1050210502.0
>
>Step   Time
>   1050310503.0
>
>Step   Time
>   1050410504.0
>
>Step   Time
>   1050510505.0
>
>Step   Time
>   1050610506.0
>
>Step   Time
>   1050710507.0
>
>Step   Time
>   1050810508.0
>
>Step   Time
>   1050910509.0
>
>Step   Time
>   1051010510.0
>
>Step   Time
>   1051110511.0
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 10512 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.2680185e+06
> Maximum force =  6.3521606e+02 on atom 4653
> Norm of force =  3.6713926e+00
>
> Should I use double precision for energy minimization?
> I need your suggestions,
>  please.
>
> Thanks
>
> Sadaf Rani
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 12/25/19 11:14 PM, Najamuddin Memon wrote:

It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.


More easily, one can identify which residues reside in loops and simply 
select by residue by using make_ndx.


-Justin


On Wed, Dec 25, 2019, 8:54 PM nupur munjal  wrote:


Hi,
i am trying to make the index file without loops and termini and using the
option protein and ligand that is 1 and 13 but the index file is formed
with the same as it is formed from the whole system.

--
Kind Regards
Nupur Munjal
PhD Scholar (Bioinformatics)
Department of Biotechnology & Bioinformatics
Jaypee University of Information Technology
Waknaghat, Solan,India

The only thing that overcomes hard luck is hard work - Harry Golden

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Najamuddin Memon]

It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.

On Wed, Dec 25, 2019, 8:54 PM nupur munjal  wrote:

> Hi,
> i am trying to make the index file without loops and termini and using the
> option protein and ligand that is 1 and 13 but the index file is formed
> with the same as it is formed from the whole system.
>
> --
> Kind Regards
> Nupur Munjal
> PhD Scholar (Bioinformatics)
> Department of Biotechnology & Bioinformatics
> Jaypee University of Information Technology
> Waknaghat, Solan,India
>
> The only thing that overcomes hard luck is hard work - Harry Golden
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> 12/25/19,
> 9:22:30 PM
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

Ok i will try, thank you so much

On Mon, 9 Dec 2019, 1:07 pm Tasneem Kausar, 
wrote:

> This problem also occurs in gromacs-5.1.4. Try higher version. We have done
> these calculations on gromacs-2016.
>
> On Mon, Dec 9, 2019 at 10:49 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > here I am using gromacs version --- gromacs-5.1.5
> >
> > On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar <
> tasneemkausa...@gmail.com>
> > wrote:
> >
> > > Please specify your gromacs version.
> > >
> > > On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> > > madhu.dhuru...@gmail.com>
> > > wrote:
> > >
> > > > hi
> > > > I am facing problem during hydrogen bond correlation c(t) with error
> > > > segmentation fault
> > > > I have used following flag for generate xtc file::- gmx trjconv -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > > > cluster
> > > > then for hydrogen bond correlation used following flag ::-gmx hbond
> -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > > > following error I am getting
> > > > Doing autocorrelation according to the theory of Luzar and Chandler.
> > > > Segmentation fault (core dumped)
> > > > please suggest me to solve this problem
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

here I am using gromacs version --- gromacs-5.1.5

On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar 
wrote:

> Please specify your gromacs version.
>
> On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > hi
> > I am facing problem during hydrogen bond correlation c(t) with error
> > segmentation fault
> > I have used following flag for generate xtc file::- gmx trjconv -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > cluster
> > then for hydrogen bond correlation used following flag ::-gmx hbond -n
> > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > following error I am getting
> > Doing autocorrelation according to the theory of Luzar and Chandler.
> > Segmentation fault (core dumped)
> > please suggest me to solve this problem
> > --
> > 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] (no subject)

[Tasneem Kausar]

Please specify your gromacs version.

On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua 
wrote:

> hi
> I am facing problem during hydrogen bond correlation c(t) with error
> segmentation fault
> I have used following flag for generate xtc file::- gmx trjconv -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> cluster
> then for hydrogen bond correlation used following flag ::-gmx hbond -n
> index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> following error I am getting
> Doing autocorrelation according to the theory of Luzar and Chandler.
> Segmentation fault (core dumped)
> please suggest me to solve this problem
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/19/19 5:55 AM, Bratin Kumar Das wrote:

Hi
 I hope there is a problem in the topology...please follow the gromacs
tutorial..


More specifically: http://www.mdtutorials.com/gmx/complex/index.html

The #include statements are out of order. You cannot add new parameters 
to the topology after any [moleculetype] has been declared. The entire 
force field must be known before any species can be introduced.


-Justin


On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:


Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:


Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to

the

system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
  ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand parameters
#include "lig.prm"

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"

I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file

for

reference.



Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

Hi
I hope there is a problem in the topology...please follow the gromacs
tutorial..

On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:

> Hi,
> Pls note that the maillist does not support attachments.
> Also it will better/helpful to use emails subject.
> Kind regards
> Alessandra
>
> On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
> wrote:
>
> > Dear All,
> > I am doing a protein-ligand simulation, when i was try to *add ions to
> the
> > system*
> > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> > *there was an error*
> > Fatal error:
> > Syntax error - File lig.prm, line 2
> > Last line read:
> > '[ bondtypes ]'
> > Invalid order for directive bondtypes
> > *my topol.top- ligand defination is as follows *
> >  ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include ligand parameters
> > #include "lig.prm"
> >
> > ; Include ligand topology
> > #include "lig.itp"
> >
> > ; Include water topology
> > #include "./charmm36-mar2019.ff/tip3p.itp"
> >
> > I have included the ligand parameter details as suggested in lig.top file
> > generated by cgenff python script. I have attached the itp and prm file
> for
> > reference.
> >
> >
> >
> > Thanks & Regards,
> > Dr. Pooja Kesari
> > Post Doctoral Fellow
> > Department Of Biosciences and Bioengineering
> > Indian Institute of Technology Bombay
> > INDIA
> > --
> > 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] (no subject)

[Alessandra Villa]

Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:

> Dear All,
> I am doing a protein-ligand simulation, when i was try to *add ions to the
> system*
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> *there was an error*
> Fatal error:
> Syntax error - File lig.prm, line 2
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
> *my topol.top- ligand defination is as follows *
>  ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand parameters
> #include "lig.prm"
>
> ; Include ligand topology
> #include "lig.itp"
>
> ; Include water topology
> #include "./charmm36-mar2019.ff/tip3p.itp"
>
> I have included the ligand parameter details as suggested in lig.top file
> generated by cgenff python script. I have attached the itp and prm file for
> reference.
>
>
>
> Thanks & Regards,
> Dr. Pooja Kesari
> Post Doctoral Fellow
> Department Of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> INDIA
> --
> 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] (no subject)

[shakuntala dhurua]

thanks Prof. Justin

On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul  wrote:

>
> Please use an appropriate subject line.
>
> On 11/12/19 5:29 AM, shakuntala dhurua wrote:
> > hello,
> > Here I want to generate arg.pdb to arg.gro by using amber99sb force
> field .
> > for test i have used 1 residue of arginine but i got Fatal error:
> > There is a dangling bond at at least one of the terminal ends and the
> force
> > field does not provide terminal entries or files. Fix your terminal
> > residues so that they match the residue database (.rtp) entries, or
> provide
> > terminal database entries (.tdb). and following is the attach pdb format
> > which i have used for pdb2gmx ,please suggest me to solve this problem
>
> AMBER does not support zwitterionic forms of single amino acids, at
> least not within GROMACS. There may be a way to create such residues
> from the AMBER parameter database, but you'll have to look into
> published works on their force field parametrization to see if such
> residue definitions exist.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] (no subject)

[shakuntala dhurua]

thanks Bratin for your suggestion

On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bra...@nitk.edu.in>
wrote:

> I think you have capped your residue in the N-terminal and C-terminal
> end...and the capping is not defined in your .rtp entry.. that's why this
> error is coming
>
> On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, 
> wrote:
>
> > hello,
> > Here I want to generate arg.pdb to arg.gro by using amber99sb force
> field .
> > for test i have used 1 residue of arginine but i got Fatal error:
> > There is a dangling bond at at least one of the terminal ends and the
> force
> > field does not provide terminal entries or files. Fix your terminal
> > residues so that they match the residue database (.rtp) entries, or
> provide
> > terminal database entries (.tdb). and following is the attach pdb format
> > which i have used for pdb2gmx ,please suggest me to solve this problem
> > --
> > 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] (no subject)

[Justin Lemkul]

Please use an appropriate subject line.

On 11/12/19 5:29 AM, shakuntala dhurua wrote:

hello,
Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
for test i have used 1 residue of arginine but i got Fatal error:
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal
residues so that they match the residue database (.rtp) entries, or provide
terminal database entries (.tdb). and following is the attach pdb format
which i have used for pdb2gmx ,please suggest me to solve this problem


AMBER does not support zwitterionic forms of single amino acids, at 
least not within GROMACS. There may be a way to create such residues 
from the AMBER parameter database, but you'll have to look into 
published works on their force field parametrization to see if such 
residue definitions exist.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

I think you have capped your residue in the N-terminal and C-terminal
end...and the capping is not defined in your .rtp entry.. that's why this
error is coming

On Tue 12 Nov, 2019, 3:58 PM shakuntala dhurua, 
wrote:

> hello,
> Here I want to generate arg.pdb to arg.gro by using amber99sb force field .
> for test i have used 1 residue of arginine but i got Fatal error:
> There is a dangling bond at at least one of the terminal ends and the force
> field does not provide terminal entries or files. Fix your terminal
> residues so that they match the residue database (.rtp) entries, or provide
> terminal database entries (.tdb). and following is the attach pdb format
> which i have used for pdb2gmx ,please suggest me to solve this problem
> --
> 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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Re: [gmx-users] (no subject)

[shakuntala dhurua]

Thank you sir for your suggestions

On Fri, 8 Nov 2019, 7:31 pm Christian Blau,  wrote:

> Hello Shakuntala,
>
>
> If you already have the trajectories, you have to post-process at least
> once to filter the data down to a manageable
> size, and once to do the periodic boundary condition fix precisely as you
> described.
>
> If you set up a new simulation you may use "nstxout-compressed" to control
> the output frequency for your xtc file. It is
> very unlikely that you will need a .trr file, so you can even set nstxout,
> nstvout and nstfout to zero. Starting your
> post-processing from a xtc should speed up your analysis process.
>
>
> On another note: Please fill in a subject line in your emails, it makes it
> easier to search and keep track of the
> ongoing discussions.
>
>
> Best,
>
> Christian
>
>
> On 11/7/19 3:12 PM, shakuntala dhurua wrote:
> > I would like to calculate rmsd of protein system, but there is much time
> > taking for trjcat of all simulated trajectories (.trr file) then
> generated
> > .xtc file by using -center -pbc mol flag. from this .xtc file i use to
> > calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
> > want to ask here is any other way is available to directly calculate rmsd
> > without using trjcat or less time taking method.
> --
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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Shakuntala,


If you already have the trajectories, you have to post-process at least once to filter the data down to a manageable 
size, and once to do the periodic boundary condition fix precisely as you described.


If you set up a new simulation you may use "nstxout-compressed" to control the output frequency for your xtc file. It is 
very unlikely that you will need a .trr file, so you can even set nstxout, nstvout and nstfout to zero. Starting your 
post-processing from a xtc should speed up your analysis process.



On another note: Please fill in a subject line in your emails, it makes it easier to search and keep track of the 
ongoing discussions.



Best,

Christian


On 11/7/19 3:12 PM, shakuntala dhurua wrote:

I would like to calculate rmsd of protein system, but there is much time
taking for trjcat of all simulated trajectories (.trr file) then generated
.xtc file by using -center -pbc mol flag. from this .xtc file i use to
calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
want to ask here is any other way is available to directly calculate rmsd
without using trjcat or less time taking method.

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Re: [gmx-users] (no subject)

[Christian Blau]

Hello Saranya,

Now again with readable formatting. Also note that it is very useful to people 
on gmx-useres to  specify the subject when writing emails, because it makes it 
easier to search, reply, and handle multiple discussion threads.

This error means that during the nvt equilibrium high forces occurred that made 
it impossible to resolve the bond constraints. The very high forces occurred 
most likely are due to some high tension in the system.

As indicated in the error message you can:
 - Reduce the time step of your run initially to relax the structure first.
 - Check the output PDB structure at the site where the error occurred (atoms 
217 and 218), possibly removing or displacing the offending water molecule 
manually
 - Check that you used a well relaxed structure from energy minimisation

Best,
Christian

On 11/1/19 7:48 AM, saranya wrote:

Hello everyone,
while running nvt equilibration i am getting the error as:
Step 12, time 0.024 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max 92522.640625 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 277278   58.90.1090  74.2482  0.1090
 281282   35.80.1098  73.5336  0.1090
 281283  119.30.1097  74.0780  0.1090
 281284   63.50.1097  74.2253  0.1090

step 12: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#

Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)



how can i resolve this error...?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*

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Re: [gmx-users] (no subject)

[blau]

Hello Saranya,This error means that during the nvt equilibrium high forces 
occurred that made it impossible to resolve the bond constraints. The very high 
forces occurred most likely are due to some high tension in the system. As 
indicated in the error message you can. Reduce the time step of your run 
initially to relax the structure first. Check the output PDB structure at the 
site where the error occurred (atoms 217 and 218), possibly removing or 
displacing the offending water molecule manually. Check that you used a well 
relaxed structure from energy minimisationBest, Christian
 Original message From: saranya  
Date: 01/11/2019  07:48  (GMT+01:00) To: gmx-us...@gromacs.org Subject: 
[gmx-users] (no subject) Hello everyone,while running nvt equilibration i am 
getting the error as:Step 12, time 0.024 (ps)  LINCS WARNINGrelative constraint 
deviation after LINCS:rms nan, max 92522.640625 (between atoms 217 and 
218)bonds that rotated more than 30 degrees: atom 1 atom 2  angle  previous, 
current, constraint length    277    278   58.9    0.1090  74.2482  0.1090  
  281    282   35.8    0.1098  73.5336  0.1090    281    283  119.3    
0.1097  74.0780  0.1090    281    284   63.5    0.1097  74.2253  
0.1090step 12: One or more water molecules can not be settled.Check for bad 
contacts and/or reduce the timestep if appropriate.Back Off! I just backed up 
step12b.pdb to ./#step12b.pdb.1#Back Off! I just backed up step12c.pdb to 
./#step12c.pdb.1#Wrote pdb files with previous and current 
coordinatesSegmentation fault (core dumped)how can i resolve this error...?With 
Regards,*Saranya Vasudevan,**Research Scholar,**Molecular Quantum Mechanics 
Laboratory,**Department of Physics,**Bharathiar University,**Coimbatore-46*-- 
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Re: [gmx-users] (no subject)

[Dallas Warren]

Look in, or search the archive, the responses are there.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/

On Mon, 30 Sep. 2019, 1:02 am Mahsa Rezaei, 
wrote:

> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
>  them.
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
>
> I made my protein-membrane system with charmm-gui.
>
> so my force is charmm36.
>
> I used the equilibration input files that charmm-gui provide ,
>
> and run 400 ns simulation for equilibration of my system .
>
> RMSD , temperature and pressure is good , so I think my system is stable .
>
> Every thing is good until I use following pull code in my mdp file .
>
> The bilayer does not move and the ligand passes through the membrane
>
> But over time , the length of the z axis increases , and
>
> 4 water molecules are also separated from the membrane.
>
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> 09/29/19,
> 06:30:36 PM
> --
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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I have seen this in Gromacs manual.

[ virtual_sites2 ]
; Site  fromfunct  a
5   1 2 1  0.7439756

for type 3 like this:

[ virtual_sites3 ]
; Site  from   funct   a  b
5   1 2 3  1   0.7439756  0.128012

for type 3fd like this:

[ virtual_sites3 ]
; Site  from   funct   a  d
5   1 2 3  2   0.5-0.105

for type 3fad like this:

[ virtual_sites3 ]
; Site  from   funct   theta  d
5   1 2 3  3   1200.5

for type 3out like this:

[ virtual_sites3 ]
; Site  from   funct   a  b  c
5   1 2 3  4   -0.4   -0.4   6.9281

for type 4fdn like this:

[ virtual_sites4 ]
; Site  from  funct   a  b  c
5   1 2 3 4   2   1.00.9   0.105

__


I have this from unk.itp file.

[ virtual_sites3 ]
; Site   from funct a   d
   52 12323 2 0   -0.164

[ exclusions ]
; ai  aj
152 1
   5223 1
   5221 1
   5222 1
   5218 1
   5219 1
   5251 1
   5250 1


Now I have to add this in topology file. Is this supposed to add in
system.top ?

On Tue, Aug 27, 2019 at 12:11 AM Justin Lemkul  wrote:

>
>
> On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
> > I can't understand meaning of this "For all other GROMACS versions, you
> > will have to manually edit the topology to use "3fad" construction and
> > appropriate atom numbers." If I am using version other than the
> > Gromacs2016.x.
> >
> > Can I get example of any topology file where these kind of
> construction've
> > for loan pair done manually in the topology file?
>
> Please see the manual for examples of what the different construction
> types are.
>
> -Justin
>
> > On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> >>> Do I have to add vsite3 information from unk.itp to system.top files?
> >> That directive belongs in the topology to which it corresponds. If it is
> >> in unk.itp, then it is already in system.top. You don't need to include
> >> anything else.
> >>
> >> -Justin
> >>
> >>> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >>>
> >>> On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >>>
>  On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn 1 to produce .tpr file using grompp command as
> mentioned
> >> in
>  Since you are getting an error rather than a warning, that means you
> are
>  not using GROMACS 2016.x, as the instructions I pointed to you say.
> 
>  If you want to use a different GROMACS version, you have to change the
>  topology. Again see the link I provided for a description of what to
> do.
> 
>  -Justin
> 
> > python script cgenff_charmm2gmx_py2.py
> >
> > output of cgenff_charmm2gmx_py2.py
> >
> >>
> _
> > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16
> (default,
>  Mar
> > 26 2019, 10:00:46)
> > [GCC 5.4.0 20160609]
> >
> > NOTE 2: Please be sure to use the same version of CGenFF in your
> > simulations that was used during parameter generation:
> > --Version of CGenFF detected in  unk.str : 4.0
> > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> >> 4.0
> > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > parameters that are already in CGenFF' option when uploading a
> molecule
> > into CGenFF.
> >
> > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
>  This
> > is not a problem, just FYI!
> >
> >  DONE 
> > Conversion complete.
> > The molecule topology has been written to unk.itp
> > Additional parameters needed by the molecule are written to unk.prm,
>  which
> > needs to be included in the system .top
> >
> > PLEASE NOTE: lone pair construction requires duplicate host atom
> >> numbers,
> > which will make grompp complain
> > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent
> this
>  check
> 
> >>
> 
> > After that I am using same -maxwarn 1 but still, it's giving error.
> It
>  may
> > be some silly 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?


Please see the manual for examples of what the different construction 
types are.


-Justin


On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:



On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:

Do I have to add vsite3 information from unk.itp to system.top files?

That directive belongs in the topology to which it corresponds. If it is
in unk.itp, then it is already in system.top. You don't need to include
anything else.

-Justin


-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:


On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned

in

Since you are getting an error rather than a warning, that means you are
not using GROMACS 2016.x, as the instructions I pointed to you say.

If you want to use a different GROMACS version, you have to change the
topology. Again see the link I provided for a description of what to do.

-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py


_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,

Mar

26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :

4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.

This

is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm,

which

needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom

numbers,

which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this

check




After that I am using same -maxwarn 1 but still, it's giving error. It

may

be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:


On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest

some

alternatives.

The link I provided before describes what you need to do. Please

consult

that information.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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send a mail to 

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

I can't understand meaning of this "For all other GROMACS versions, you
will have to manually edit the topology to use "3fad" construction and
appropriate atom numbers." If I am using version other than the
Gromacs2016.x.

Can I get example of any topology file where these kind of construction've
for loan pair done manually in the topology file?

On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul  wrote:

>
>
> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> > Do I have to add vsite3 information from unk.itp to system.top files?
>
> That directive belongs in the topology to which it corresponds. If it is
> in unk.itp, then it is already in system.top. You don't need to include
> anything else.
>
> -Justin
>
> > -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >
> > On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:
> >
> >>
> >> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>> Yeah! I have read that.
> >>>
> >>> uses -maxwarn 1 to produce .tpr file using grompp command as mentioned
> in
> >> Since you are getting an error rather than a warning, that means you are
> >> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>
> >> If you want to use a different GROMACS version, you have to change the
> >> topology. Again see the link I provided for a description of what to do.
> >>
> >> -Justin
> >>
> >>> python script cgenff_charmm2gmx_py2.py
> >>>
> >>> output of cgenff_charmm2gmx_py2.py
> >>>
> >>
> _
> >>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> >> Mar
> >>> 26 2019, 10:00:46)
> >>> [GCC 5.4.0 20160609]
> >>>
> >>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>> simulations that was used during parameter generation:
> >>> --Version of CGenFF detected in  unk.str : 4.0
> >>> --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc :
> 4.0
> >>>
> >>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>> parameters that are already in CGenFF' option when uploading a molecule
> >>> into CGenFF.
> >>>
> >>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >> This
> >>> is not a problem, just FYI!
> >>>
> >>>  DONE 
> >>> Conversion complete.
> >>> The molecule topology has been written to unk.itp
> >>> Additional parameters needed by the molecule are written to unk.prm,
> >> which
> >>> needs to be included in the system .top
> >>>
> >>> PLEASE NOTE: lone pair construction requires duplicate host atom
> numbers,
> >>> which will make grompp complain
> >>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> >> check
> >>
> 
> >>> After that I am using same -maxwarn 1 but still, it's giving error. It
> >> may
> >>> be some silly mistake please let me know.
> >>>
> >>>
> >>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >>>
>  On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > Thank You Sir!
> >
> > Attached file can be downloaded from following link.
> >
> > https://fil.email/OR7Nsh0f
> > 
> > 
> > Error
> >
> > ERROR 1 [file unk.itp, line 497]:
> >  Duplicate atom index (23) in virtual_sites3
> > ___
> >
> > It support lone pair construction for halogens only. Please suggest
> >> some
> > alternatives.
>  The link I provided before describes what you need to do. Please
> consult
>  that information.
> 
>  -Justin
> 
>  --
>  ==
> 
>  Justin A. Lemkul, Ph.D.
>  Assistant Professor
>  Office: 301 Fralin Hall
>  Lab: 303 Engel Hall
> 
>  Virginia Tech Department of Biochemistry
>  340 West Campus Dr.
>  Blacksburg, VA 24061
> 
>  jalem...@vt.edu | (540) 231-3129
>  http://www.thelemkullab.com
> 
>  ==
> 
>  --
>  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.
> 
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:

Do I have to add vsite3 information from unk.itp to system.top files?


That directive belongs in the topology to which it corresponds. If it is 
in unk.itp, then it is already in system.top. You don't need to include 
anything else.


-Justin


-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:



On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in

Since you are getting an error rather than a warning, that means you are
not using GROMACS 2016.x, as the instructions I pointed to you say.

If you want to use a different GROMACS version, you have to change the
topology. Again see the link I provided for a description of what to do.

-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py


_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,

Mar

26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.

This

is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm,

which

needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this

check


After that I am using same -maxwarn 1 but still, it's giving error. It

may

be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:


On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
 Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest

some

alternatives.

The link I provided before describes what you need to do. Please consult
that information.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Do I have to add vsite3 information from unk.itp to system.top files?

-maxwarn 1 flag I checked in gromacs 16 version and it's running there.

On Mon, 26 Aug 2019, 00:58 Justin Lemkul,  wrote:

>
>
> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> > Yeah! I have read that.
> >
> > uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
>
> Since you are getting an error rather than a warning, that means you are
> not using GROMACS 2016.x, as the instructions I pointed to you say.
>
> If you want to use a different GROMACS version, you have to change the
> topology. Again see the link I provided for a description of what to do.
>
> -Justin
>
> > python script cgenff_charmm2gmx_py2.py
> >
> > output of cgenff_charmm2gmx_py2.py
> >
> _
> >
> > NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default,
> Mar
> > 26 2019, 10:00:46)
> > [GCC 5.4.0 20160609]
> >
> > NOTE 2: Please be sure to use the same version of CGenFF in your
> > simulations that was used during parameter generation:
> > --Version of CGenFF detected in  unk.str : 4.0
> > --Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0
> >
> > NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> > parameters that are already in CGenFF' option when uploading a molecule
> > into CGenFF.
> >
> > NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> This
> > is not a problem, just FYI!
> >
> >  DONE 
> > Conversion complete.
> > The molecule topology has been written to unk.itp
> > Additional parameters needed by the molecule are written to unk.prm,
> which
> > needs to be included in the system .top
> >
> > PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
> > which will make grompp complain
> > To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this
> check
> >
> 
> >
> > After that I am using same -maxwarn 1 but still, it's giving error. It
> may
> > be some silly mistake please let me know.
> >
> >
> > On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:
> >
> >>
> >> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>> Thank You Sir!
> >>>
> >>> Attached file can be downloaded from following link.
> >>>
> >>> https://fil.email/OR7Nsh0f
> >>> 
> >>> 
> >>> Error
> >>>
> >>> ERROR 1 [file unk.itp, line 497]:
> >>> Duplicate atom index (23) in virtual_sites3
> >>> ___
> >>>
> >>> It support lone pair construction for halogens only. Please suggest
> some
> >>> alternatives.
> >> The link I provided before describes what you need to do. Please consult
> >> that information.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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.
> >>
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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] (no subject)

[Justin Lemkul]

On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in


Since you are getting an error rather than a warning, that means you are 
not using GROMACS 2016.x, as the instructions I pointed to you say.


If you want to use a different GROMACS version, you have to change the 
topology. Again see the link I provided for a description of what to do.


-Justin


python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py
_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default, Mar
26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file. This
is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm, which
needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check


After that I am using same -maxwarn 1 but still, it's giving error. It may
be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:



On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.

The link I provided before describes what you need to do. Please consult
that information.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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

Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Yeah! I have read that.

uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in
python script cgenff_charmm2gmx_py2.py

output of cgenff_charmm2gmx_py2.py
_

NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16 (default, Mar
26 2019, 10:00:46)
[GCC 5.4.0 20160609]

NOTE 2: Please be sure to use the same version of CGenFF in your
simulations that was used during parameter generation:
--Version of CGenFF detected in  unk.str : 4.0
--Version of CGenFF detected in  charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

NOTE 4: 1 lone pairs found in topology that are not in the mol2 file. This
is not a problem, just FYI!

 DONE 
Conversion complete.
The molecule topology has been written to unk.itp
Additional parameters needed by the molecule are written to unk.prm, which
needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers,
which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check


After that I am using same -maxwarn 1 but still, it's giving error. It may
be some silly mistake please let me know.


On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> > Thank You Sir!
> >
> > Attached file can be downloaded from following link.
> >
> > https://fil.email/OR7Nsh0f
> > 
> > 
> > Error
> >
> > ERROR 1 [file unk.itp, line 497]:
> >Duplicate atom index (23) in virtual_sites3
> > ___
> >
> > It support lone pair construction for halogens only. Please suggest some
> > alternatives.
>
> The link I provided before describes what you need to do. Please consult
> that information.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
   Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.


The link I provided before describes what you need to do. Please consult 
that information.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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Re: [gmx-users] (no subject)

[Navneet Kumar Singh]

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f


Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___

It support lone pair construction for halogens only. Please suggest some
alternatives.

On Sun, Aug 25, 2019 at 8:11 PM Justin Lemkul  wrote:

>
>
> On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:
> > can you please help in solving this error while running MD simulation of
> > protein-ligand complex using CHARMM36 force field on GROMACS engine.
> >
> >
> >
> > *Command*
> >
> > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*
> >
> >
> > *ERROR*
> >
> >
> > *ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
> > virtual_sites3*
> >
> >
> >
> **
> >
> > *unk.itp file indicated error/ Please find the attached file for more
> > details.*
>
> The mailing list does not accept attachments.
>
> Please see the information at
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which
> specifically addresses this lone pair issue and how to deal with it.
> GROMACS does not easily support the kinds of lone pair/vsite
> construction that CHARMM requires for this kind of interaction.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>


-- 






 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  

 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:

can you please help in solving this error while running MD simulation of
protein-ligand complex using CHARMM36 force field on GROMACS engine.



*Command*

*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*


*ERROR*


*ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
virtual_sites3*


**

*unk.itp file indicated error/ Please find the attached file for more
details.*


The mailing list does not accept attachments.

Please see the information at 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which 
specifically addresses this lone pair issue and how to deal with it. 
GROMACS does not easily support the kinds of lone pair/vsite 
construction that CHARMM requires for this kind of interaction.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/19/19 2:00 AM, Priyanka Singh wrote:

Hii
I am new to simulations. I want to ask is it ok to use ligand topology
build using PRODRG server if using amber force field for RNA-ligand
simulation. what precautions one should take ends of the RNA molecule.
PRODRG is for GROMOS and produces very low-quality topologies. You 
cannot combine GROMOS topologies with AMBER (nor can you mix and match 
any force fields). Do everything with one force field. AMBER + GAFF is a 
much better option.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Jorden Cabal]

I think the answer is not so straightforward. It depends upon a lot of
things, but I would say that the parameters derived using QM is better. If
you do not have any other options you can still use PRODRG server but even
in that case, I find many people using the docked (or bound) conformation
of the Ligand molecule to generate the initial parameters, which in my view
should not be done. One should generate the parameters using the molecule
in its minimum energy conformation instead of bound conformation.
I would also suggest you to look at the RED server. Please follow this link
https://upjv.q4md-forcefieldtools.org/RED/

Thank you

On Mon, Aug 19, 2019 at 3:00 PM Priyanka Singh 
wrote:

> Hii
> I am new to simulations. I want to ask is it ok to use ligand topology
> build using PRODRG server if using amber force field for RNA-ligand
> simulation. what precautions one should take ends of the RNA molecule.
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Re: [gmx-users] (no subject) (Soham Sarkar)

[Soham Sarkar]

Hello,
 The "?" You are talking about is mistakenly written there. The
original itp file has nothing there and is showing the error. The first few
lines are commented out. So why is that problem? Sorry for not giving a
title. If you want, I can share the original itp file here but as per the
rule I can not attach any sort of files here. So now please tell me what
could be the problem?

On Fri, 5 Apr 2019, 3:26 pm ABEL Stephane,  wrote:

> Hi
>
> In your itp you have a "?"
>
> ?; GENERATED BY LigParGen Server
>
> Remove it and the problem will be solved
>
> PS : next time add a title in you message.
>
> Good luck
>
> -
> --
>
> Message: 1
> Date: Fri, 5 Apr 2019 14:26:00 +0530
> From: Soham Sarkar 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] (no subject)
> Message-ID:
> <
> ca+fbedfs1gay1d5k-zvdv9fgmzxfenf-ia-mwetruuqbwpm...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
> I am using GROMACS-2018. I want to simulate a system which contain
> Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
> the GROMPP command. I have defined this residue in aminoacids.rtp.
>
> The error is like
>
> "NOTE 1 [file ions.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 918407885
>
> WARNING 1 [file tba.itp, line 1]:
>   Too few gb parameters for type ?
>
>
> Couldn't find topology match for atomtype ?
> Aborted (core dumped)"
>  I have generated the itp file for TBA from ligpargen.
>
> My itp file is
>
> ;
> ?; GENERATED BY LigParGen Server
> ; Jorgensen Lab @ Yale University
> ;
>
> [ atomtypes ]
>   opls_135C112.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H11 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H12 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H13 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_159C212.0110 0.000A3.5E-01   2.76144E-01
>   opls_135C312.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H31 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H32 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H33 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_154O415.9990 0.000A3.12000E-01   7.11280E-01
>   opls_155   H41 1.0080 0.000A0.0E+00   0.0E+00
>   opls_135C512.0110 0.000A3.5E-01   2.76144E-01
>   opls_140   H51 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H52 1.0080 0.000A2.5E-01   1.25520E-01
>   opls_140   H53 1.0080 0.000A2.5E-01   1.25520E-01
>
> [ moleculetype ]
> ; Name   nrexcl
> TBA   3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
>  1   opls_135  1TBAC1  1-0.304408  12.0110
>  2   opls_140  1TBA   H11  1 0.098297   1.0080
>  3   opls_140  1TBA   H12  1 0.086235   1.0080
>  4   opls_140  1TBA   H13  1 0.111410   1.0080
>  5   opls_159  1TBAC2  1 0.247098  12.0110
>  6   opls_135  1TBAC3  1-0.299728  12.0110
>  7   opls_140  1TBA   H31  1 0.101177   1.0080
>  8   opls_140  1TBA   H32  1 0.110693   1.0080
>  9   opls_140  1TBA   H33  1 0.110695   1.0080
> 10   opls_154  1TBAO4  1-0.550587  15.9990
> 11   opls_155  1TBA   H41  1 0.297574   1.0080
> 12   opls_135  1TBAC5  1-0.304401  12.0110
> 13   opls_140  1TBA   H51  1 0.098298   1.0080
> 14   opls_140  1TBA   H52  1 0.086234   1.0080
> 15   opls_140  1TBA   H53  1 0.111413   1.0080
> [ bonds ]
> 2 1 1  0.1090 284512.000
> 3 1 1  0.1090 284512.000
> 4 1 1  0.1090 284512.000
> 5 1 1  0.1529 224262.400
> 6 5 1  0.1529 224262.400
> 7 6 1  0.1090 284512.000
> 8 6 1  0.1090 284512.000
> 9 6 1  0.1090 284512.000
>10 5 1  0.1410 267776.000
>1110 1  0.0945 462750.400
>12 5 1  0.1529 224262.400
>1312 1  0.1090 284512.000
>1412 1  0.1090 284512.000
>1512 1  0.1090 284512.000
>
> [ angles ]
> ;  aiajak functc0c1
> c2c3
> 2 1 3 1107.800276.144
> 2 1 4 1107.800276.144
> 2 1 5 1110.700313.800
> 1 5 6 1112.700

Re: [gmx-users] (no subject)

[Dallas Warren]

In molecular dynamics things move around.

The fact that the molecules aren't in the starting position shows that it
isn't a stable configuration, the interactions between the protein and the
molecules are insufficient to keep them together in that spot.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 28 Mar 2019 at 05:50, saranya  wrote:

> Hi users,
>
>   I have simulated a protein with gas molecules (CO2,NO2 and SO2) for
> 100ns. I have followed the  protein ligand tutorial. I have applied
> position constraints. After equilibrium the gas molecules are at the docked
> position but at the 60ns simulation the gas molecules are far away from the
> protein. I have applied pBC and sure this is not an visualisatuin error.
> How can I rectify this, Kindly give your valuable suggestions in this
> regard.
>
>
>
> --
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
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Re: [gmx-users] (no subject)

[Dallas Warren]

http://manual.gromacs.org/documentation/current/reference-manual/topologies/force-field-organization.html

FFs are located in the share/gromacs/top directory.  If you have your own
FF that isn't included in the distribution with GROMACS, you can either add
it to that directory, or have the FF directory within the directory you run
the simulation.  Then you simply refer the links in your topology files to
that location.

Or are you asking how you can solvate your molecule within ethanol, so you
have it located in an ethanol solution, then run the simulation?  See
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sat, 9 Feb 2019 at 05:30, Satya Ranjan Sahoo 
wrote:

> Sir,
> Can anyone suggest how I can use ethanol force field to solvate and run MD
> for my molecule. Please help.
>
> On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo  wrote:
>
> > Sir,
> > I am a beginner to GROMACS. I was unable to understand how to create all
> > the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> > nvt.mdp , porse.itp , topol.top input files for molecular simulation of
> my
> > molecule. Please teach me how can I generate or create all the above
> > mentioned input files for my molecule.
> >
> --
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Re: [gmx-users] (no subject)

[Satya Ranjan Sahoo]

Sir,
Can anyone suggest how I can use ethanol force field to solvate and run MD
for my molecule. Please help.

On Thu 31 Jan, 2019, 10:48 AM Satya Ranjan Sahoo  Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> nvt.mdp , porse.itp , topol.top input files for molecular simulation of my
> molecule. Please teach me how can I generate or create all the above
> mentioned input files for my molecule.
>
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Re: [gmx-users] (no subject)

[pbuscemi]

Run the tutorials

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Satya
Ranjan Sahoo
Sent: Wednesday, January 30, 2019 11:19 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] (no subject)

Sir,
I am a beginner to GROMACS. I was unable to understand how to create all the
ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp , nvt.mdp ,
porse.itp , topol.top input files for molecular simulation of my molecule.
Please teach me how can I generate or create all the above mentioned input
files for my molecule.
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Re: [gmx-users] (no subject)

[Saumyak Mukherjee]

Hi,

There is a detailed online tutorial.
http://www.mdtutorials.com/gmx/

It has everything you need.

Best,
Saumyak

On Thu, 31 Jan 2019 at 10:51, Satya Ranjan Sahoo 
wrote:

> Sir,
> I am a beginner to GROMACS. I was unable to understand how to create all
> the ions.mdp , md.mdp , mout.mdp , minim.mdp , newbox.mdp , npt.mdp ,
> nvt.mdp , porse.itp , topol.top input files for molecular simulation of my
> molecule. Please teach me how can I generate or create all the above
> mentioned input files for my molecule.
> --
> 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.
>


-- 
===
*Saumyak Mukherjee*
Senior Research Fellow
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bengaluru - 560012
===
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

This is one of the examples in the documentation of gmx select. Try looking
there!

Mark

On Fri., 25 Jan. 2019, 07:30 Soham Sarkar,  wrote:

> Hello Everyone,
>I want to calculate some properties of the solvent molecules within
> 6angstrom from the protein backbone, for that I need a index group which
> only contain that number of solvent molecules in the index.ndx file so that
> I can specifically select that index to calculate different parameters.
> Please any one help me how would I do that?
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 12/1/18 8:11 AM, Soham Sarkar wrote:

Dear all,
This is the error I get while executing the grompp command
  " Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
 "
I am attaching the input files. I have generated the tris.itp from tppmktop


Attachments are not allowed on the mailing list.

There are several things to consider. The first is that version 4.5.6 is 
ancient and no longer supported. Use a modern GROMACS version. The 
second is to look at what is in the topology on line 19 to see how not 
to trigger the error that you're getting.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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==

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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/23/18 12:58 AM, maya nair wrote:

I am trying to do the molecular dynamics of  DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp  ions.mdp and em.mdp, it gives error saying the following

Command line:
   gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
   Too few gb parameters for type 1


Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.


The .atp file is only read by pdb2gmx, so it's not relevant. Apparently 
you have an atom type "1" (number one) in your topology, which is very 
strange. It doesn't have parameters defined in gb.itp, so you get a 
failure. Make sure your input is sound and your topology/force field 
files are free of typos.



Help me in this regard. I am attaching my files.


This mailing list does not accept attachments. If you need to share 
files, use a file-sharing service and provide the URL.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/23/18 12:11 PM, AKANXA TIWARI wrote:

Hi
During simulation of protein after giving grompp ions command i got a note
what should i do.
  NOTE 3 [file ions2.mdp]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider using PME electrostatics.


This note is harmless if the .tpr file is only being used to add ions. 
Trying to use PME (e.g. by copying an .mdp file that is used for EM or 
MD) will trigger a fatal error due to the non-zero charge of the system. 
So .mdp files specifying plain cutoffs are necessary for adding ions, 
but should not be used for anything else.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

In your .mdp file ...in cut-off you mention PME...

On Sun, Sep 23, 2018, 9:42 PM AKANXA TIWARI 
wrote:

> Hi
> During simulation of protein after giving grompp ions command i got a note
> what should i do.
>  NOTE 3 [file ions2.mdp]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
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Re: [gmx-users] (no subject)

[Vytautas Rakeviius]

 I suggest this tool:https://github.com/llazzaro/acpype 

On Friday, September 14, 2018, 10:44:56 PM GMT+3, SAKO MIRZAIE 
 wrote:  
 
 Hi every one,
I need the topology parameters for pyridoxal phosphate linked to lysine
with amber99sb force field. does anyone have the mentioned parameters? I
searched it among publications but I didn't find it at all.

Best regards,

-- 
***
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/_Academician?username=sakomirzaie

http://www.iausdj.ac.ir/_Academician/English?username=sakomirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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Re: [gmx-users] (no subject)

[AKANXA TIWARI]

thanks for reply


On Fri, Sep 14, 2018 at 5:09 PM Justin Lemkul  wrote:

>
>
> On 9/14/18 6:48 AM, AKANXA TIWARI wrote:
> > i am getting a warning after converting pdb2gmx and then applying force
> > field what i will do. please help me.i get this on screen.
> > WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> > mapped
> > to an entry in the topology database, but the atom H used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
> >
> >
> > WARNING: WARNING: Residue 374 named PHE of a molecule in the input file
> was
> > mapped
> > to an entry in the topology database, but the atom O used in
> > an interaction of type angle in that entry is not found in the
> > input file. Perhaps your atom and/or residue naming needs to be
> > fixed.
> >
>
> pdb2gmx is just being a bit too noisy here. Termini are being patched,
> which means some atoms get deleted, replaced, or added. Here, an
> existing atom is being deleted and replaced with another at both the N-
> and C-termini. There is no problem, as you see the message below about
> successful completion.
>
> -Justin
>
> > Before cleaning: 6050 pairs
> > Before cleaning: 7868 dihedrals
> > Making cmap torsions...
> > There are 2709 dihedrals, 1833 impropers, 5404 angles
> >6050 pairs, 3705 bonds and 0 virtual sites
> > Total mass 40604.576 a.m.u.
> > Total charge 11.000 e
> > Writing topology
> >
> > Back Off! I just backed up posre.itp to ./#posre.itp.1#
> >
> > Writing coordinate file...
> >
> > Back Off! I just backed up actin_asp_processed.gro to
> > ./#actin_asp_processed.gro.1#
> >  - PLEASE NOTE 
> > You have successfully generated a topology from: actin_asp_clean.pdb.
> > The Gromos54a7 force field and the spce water model are used.
> >  - ETON ESAELP 
> >
> > GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
> >
> > akanxa@akanxa-HP-Notebook:~/Documents/aasp$
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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] (no subject)

[Justin Lemkul]

On 9/14/18 6:48 AM, AKANXA TIWARI wrote:

i am getting a warning after converting pdb2gmx and then applying force
field what i will do. please help me.i get this on screen.
WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



pdb2gmx is just being a bit too noisy here. Termini are being patched, 
which means some atoms get deleted, replaced, or added. Here, an 
existing atom is being deleted and replaced with another at both the N- 
and C-termini. There is no problem, as you see the message below about 
successful completion.


-Justin


Before cleaning: 6050 pairs
Before cleaning: 7868 dihedrals
Making cmap torsions...
There are 2709 dihedrals, 1833 impropers, 5404 angles
   6050 pairs, 3705 bonds and 0 virtual sites
Total mass 40604.576 a.m.u.
Total charge 11.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...

Back Off! I just backed up actin_asp_processed.gro to
./#actin_asp_processed.gro.1#
 - PLEASE NOTE 
You have successfully generated a topology from: actin_asp_clean.pdb.
The Gromos54a7 force field and the spce water model are used.
 - ETON ESAELP 

GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)

akanxa@akanxa-HP-Notebook:~/Documents/aasp$


--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

You need to add the particular H to the amino acid .rtp file in the
forcefield folder

On Fri, Sep 14, 2018, 4:24 PM AKANXA TIWARI 
wrote:

> i am getting a warning after converting pdb2gmx and then applying force
> field what i will do. please help me.i get this on screen.
> WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
>
> WARNING: WARNING: Residue 374 named PHE of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 6050 pairs
> Before cleaning: 7868 dihedrals
> Making cmap torsions...
> There are 2709 dihedrals, 1833 impropers, 5404 angles
>   6050 pairs, 3705 bonds and 0 virtual sites
> Total mass 40604.576 a.m.u.
> Total charge 11.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.1#
>
> Writing coordinate file...
>
> Back Off! I just backed up actin_asp_processed.gro to
> ./#actin_asp_processed.gro.1#
> - PLEASE NOTE 
> You have successfully generated a topology from: actin_asp_clean.pdb.
> The Gromos54a7 force field and the spce water model are used.
> - ETON ESAELP 
>
> GROMACS reminds you: "Miggida-Miggida-Miggida-Mac" (Kriss Kross)
>
> akanxa@akanxa-HP-Notebook:~/Documents/aasp$
> --
> 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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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/10/18 9:14 AM, Bratin Kumar Das wrote:

Use -maxwarn 2 at the last of your gmx grompp ... command


No! One should *never* use -maxwarn just to circumvent problems. It is 
clear that there is some modification to ffnonbonded.itp that is 
syntactically incorrect. grompp will not have the right parameters and 
any process that tries to use this .tpr file will fail.


-Justin


On Mon, Sep 10, 2018, 6:19 PM saranya  wrote:


Dear Users,

 My simulation system is Amyloid β Protein (1-42) with Fe2+ complex
and i am using OPLSAA forcefield for the simulations. I edited the
ffbonded.itp files accordingly as mentioned in the tutorials.

While running grompp command, I get following error:



gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr

   :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:



 GROMACS is written by:

  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar

  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch

   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
Hindriksen

  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff

Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk

Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers

Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf

and the project leaders:

 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel



Copyright (c) 1991-2000, University of Groningen, The Netherlands.

Copyright (c) 2001-2015, The GROMACS development team at

Uppsala University, Stockholm University and

the Royal Institute of Technology, Sweden.

check out http://www.gromacs.org for more information.



GROMACS is free software; you can redistribute it and/or modify it

under the terms of the GNU Lesser General Public License

as published by the Free Software Foundation; either version 2.1

of the License, or (at your option) any later version.



GROMACS:  gmx grompp, VERSION 5.1.2

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

   gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr



Ignoring obsolete mdp entry 'title'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

Setting the LD random seed to 2295799000



WARNING 1 [file ffnonbonded.itp, line 3]:

   Too few parameters on line (source file

   /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,

   line 283)



Generated 335790 of the 335790 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 335790 of the 335790 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

Excluding 2 bonded neighbours molecule type 'SOL'



NOTE 1 [file c5.top, line 5912]:

   System has non-zero total charge: -2.00

   Total charge should normally be an integer. See

   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

   for discussion on how close it should be to an integer.







Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:42Protein residues

There are: 1  Other residues

There are:  8015  Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

Number of degrees of freedom in T-Coupling group rest is 49971.00

Calculating fourier grid dimensions for X Y Z

Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113

Estimate for the relative computational load of the PME mesh part: 0.23

This run will generate roughly 2 Mb of data



There was 1 note



There was 1 warning



---

Program gmx grompp, VERSION 5.1.2

Source code file:
/home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c,
line: 2107



Fatal error:

Too many warnings (1), gmx terminated.

If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---



Anyone can help me in overcoming this fatal error will be appreciated.





With Regards,

Saranya Vasudevan,

Research Scholar,

Molecular Quantum Mechanics Laboratory,

Department of Physics,

Bharathiar University,

Coimbatore-46
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--

Re: [gmx-users] (no subject)

[Bratin Kumar Das]

Use -maxwarn 2 at the last of your gmx grompp ... command

On Mon, Sep 10, 2018, 6:19 PM saranya  wrote:

> Dear Users,
>
> My simulation system is Amyloid β Protein (1-42) with Fe2+ complex
> and i am using OPLSAA forcefield for the simulations. I edited the
> ffbonded.itp files accordingly as mentioned in the tutorials.
>
> While running grompp command, I get following error:
>
>
>
> gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr
>
>   :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
>
>
>
> GROMACS is written by:
>
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>
>  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
>
>   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
> Hindriksen
>
>  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
>
> Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
>
>Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>
>Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
>
>Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>
>and the project leaders:
>
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
>
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>
> Copyright (c) 2001-2015, The GROMACS development team at
>
> Uppsala University, Stockholm University and
>
> the Royal Institute of Technology, Sweden.
>
> check out http://www.gromacs.org for more information.
>
>
>
> GROMACS is free software; you can redistribute it and/or modify it
>
> under the terms of the GNU Lesser General Public License
>
> as published by the Free Software Foundation; either version 2.1
>
> of the License, or (at your option) any later version.
>
>
>
> GROMACS:  gmx grompp, VERSION 5.1.2
>
> Executable:   /usr/local/gromacs/bin/gmx
>
> Data prefix:  /usr/local/gromacs
>
> Command line:
>
>   gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr
>
>
>
> Ignoring obsolete mdp entry 'title'
>
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>
> Setting the LD random seed to 2295799000
>
>
>
> WARNING 1 [file ffnonbonded.itp, line 3]:
>
>   Too few parameters on line (source file
>
>   /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,
>
>   line 283)
>
>
>
> Generated 335790 of the 335790 non-bonded parameter combinations
>
> Generating 1-4 interactions: fudge = 0.5
>
> Generated 335790 of the 335790 1-4 parameter combinations
>
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>
> Excluding 2 bonded neighbours molecule type 'SOL'
>
>
>
> NOTE 1 [file c5.top, line 5912]:
>
>   System has non-zero total charge: -2.00
>
>   Total charge should normally be an integer. See
>
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>
>   for discussion on how close it should be to an integer.
>
>
>
>
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
> Analysing residue names:
>
> There are:42Protein residues
>
> There are: 1  Other residues
>
> There are:  8015  Water residues
>
> Analysing Protein...
>
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
> Number of degrees of freedom in T-Coupling group rest is 49971.00
>
> Calculating fourier grid dimensions for X Y Z
>
> Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113
>
> Estimate for the relative computational load of the PME mesh part: 0.23
>
> This run will generate roughly 2 Mb of data
>
>
>
> There was 1 note
>
>
>
> There was 1 warning
>
>
>
> ---
>
> Program gmx grompp, VERSION 5.1.2
>
> Source code file:
> /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c,
> line: 2107
>
>
>
> Fatal error:
>
> Too many warnings (1), gmx terminated.
>
> If you are sure all warnings are harmless, use the -maxwarn option.
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
>
> Anyone can help me in overcoming this fatal error will be appreciated.
>
>
>
>
>
> 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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* Please search the archive at 

Re: [gmx-users] (no subject)

[Rakesh Mishra]

Dear  Mark,

I think things are not under solution.

Please tell me if there is  dsDNA of chain A (12 bp)
and  complimentary strand B(12 bp)  like

chain A-   3' - 5'
chain B-   5' - 3'
I am pulling   5' end  of strand  A and made 5' of B as a reference group
along the helical direction under constant velocity pulling. And both the
chains are free ( no restraint) ,
under this situation will the 5' of chain B (act as reference group) feel
the equal and opposite force like 5' end of chain A where pulling is
applied .
Due to this equal and opposite force both the strand will move opposite to
each other or not .



On Mon, Sep 3, 2018 at 10:00 AM, Rakesh Mishra  wrote:

> Hi Mark
>
> Did you get the point or  not .
> Hoping your  response
>
> On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra 
> wrote:
>
>>
>> *Please remember (its your  query to me )*
>> Hi,
>>
>> Can you please share a link to something that indicates why this would be
>> a
>> good tool for modeling such experimental pulling scenarios? Making the
>> case
>> for implementing such a feature would benefit from that.
>>
>> Mark
>> > > dt)+-+t2,+e=gmail=g
>> 
>> >
>>
>>
>>
>> *This is our response *
>>
>>
>> Dear Mark,
>>
>> There are several experiments have been done for protein and DNA
>> unfolding.
>> Thy  became pioneer in this field.  That is why force should apply and
>> corresponding reaction
>> coordinates are measured . Here Gromacs login do not allow to upload
>> larger data.
>> But I can mention some paper address . If get time Please go through
>> these papers .
>>
>> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
>> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>>
>> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
>> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>>
>> That is  why I  asked about force-extension protocol.  In Umbrella
>> sampling distance is increases linearly with the time and corresponding
>> force experienced by the system writes .
>>
>> We still don't no that force/time which writes in .xvg file corresponds
>> which formula like f= k(vt-x) or something else.
>> There are other lot experiments regarding measurement of stability of the
>> DNA and protein under f/x curve.
>> One can see some theory paper also to see f/x like.
>>
>> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>>
>>
>>
>>
>> Note- According to Justin one  can write that protocol. If suppose we
>> write that protocol, then how  to apply in gromacs.
>>
>> There are only input .mdp files. We didn't know  where to built the force
>> subroutine in .ff (force field ) directory. or somewhere else.
>>
>>
>> Hoping for  response.
>>
>>
>>
>>
>>
>>
>> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra 
>> wrote:
>>
>>> Dear  mark
>>> I had already discussed regarding force/extension protocol.
>>> But I didn't get any response from your side. I dont have
>>> idea to upload some pictures.
>>>
>>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
>>> wrote:
>>>
 Hi,

 The list cannot accept attachments. Upload to a file sharing service and
 share a link. We will likely need more background information also.

 Mark

 On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:

 > Hi every body
 > can any one  explain what is the mean of this graph
 > obtained from gromacs  constant velocity pulling of dsDNA
 > along the helical direction. (force.xvg). Basically sudden drop of
 force
 > represents what ?
 > --
 > Gromacs Users mailing list
 >
 > * Please search the archive at
 > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 > posting!
 >
 > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >
 > * For (un)subscribe requests visit
 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 > send a mail to gmx-users-requ...@gromacs.org.
 --
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 * 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.

>>>
>>>
>>>
>>> --
>>>
>>> *With Best-Rakesh Kumar Mishra*
>>> *  (RA)CSD  SINP Kolkata, India*
>>>
>>> *E-mail - rakesh.mis...@saha.ac.in  *
>>>
>>> *Phone n. +91 9473662491, +918777496532*
>>>
>>
>>
>>
>> --
>>
>> *With Best-Rakesh Kumar Mishra*
>> *  (RA)CSD  SINP Kolkata, India*
>>
>> *E-mail - rakesh.mis...@saha.ac.in  *
>>
>> *Phone n. +91 9473662491, +918777496532*
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *

Re: [gmx-users] (no subject)

[Rakesh Mishra]

Hi Mark

Did you get the point or  not .
Hoping your  response

On Fri, Aug 31, 2018 at 6:17 PM, Rakesh Mishra  wrote:

>
> *Please remember (its your  query to me )*
> Hi,
>
> Can you please share a link to something that indicates why this would be a
> good tool for modeling such experimental pulling scenarios? Making the case
> for implementing such a feature would benefit from that.
>
> Mark
> >  dt)+-+t2,+e=gmail=g
> 
> >
>
>
>
> *This is our response *
>
>
> Dear Mark,
>
> There are several experiments have been done for protein and DNA
> unfolding.
> Thy  became pioneer in this field.  That is why force should apply and
> corresponding reaction
> coordinates are measured . Here Gromacs login do not allow to upload
> larger data.
> But I can mention some paper address . If get time Please go through these
> papers .
>
> 1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
> Bustamante*†, Zev Bryant* & Steven B. Smith†)
>
> 2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
> Oesterhelt, Berthold Heymann,Hermann E. Gaub )
>
> That is  why I  asked about force-extension protocol.  In Umbrella
> sampling distance is increases linearly with the time and corresponding
> force experienced by the system writes .
>
> We still don't no that force/time which writes in .xvg file corresponds
> which formula like f= k(vt-x) or something else.
> There are other lot experiments regarding measurement of stability of the
> DNA and protein under f/x curve.
> One can see some theory paper also to see f/x like.
>
> 1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)
>
>
>
>
> Note- According to Justin one  can write that protocol. If suppose we
> write that protocol, then how  to apply in gromacs.
>
> There are only input .mdp files. We didn't know  where to built the force
> subroutine in .ff (force field ) directory. or somewhere else.
>
>
> Hoping for  response.
>
>
>
>
>
>
> On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra 
> wrote:
>
>> Dear  mark
>> I had already discussed regarding force/extension protocol.
>> But I didn't get any response from your side. I dont have
>> idea to upload some pictures.
>>
>> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> The list cannot accept attachments. Upload to a file sharing service and
>>> share a link. We will likely need more background information also.
>>>
>>> Mark
>>>
>>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:
>>>
>>> > Hi every body
>>> > can any one  explain what is the mean of this graph
>>> > obtained from gromacs  constant velocity pulling of dsDNA
>>> > along the helical direction. (force.xvg). Basically sudden drop of
>>> force
>>> > represents what ?
>>> > --
>>> > 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.
>>> --
>>> 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.
>>>
>>
>>
>>
>> --
>>
>> *With Best-Rakesh Kumar Mishra*
>> *  (RA)CSD  SINP Kolkata, India*
>>
>> *E-mail - rakesh.mis...@saha.ac.in  *
>>
>> *Phone n. +91 9473662491, +918777496532*
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491, +918777496532*
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
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Re: [gmx-users] (no subject)

[Rakesh Mishra]

*Please remember (its your  query to me )*
Hi,

Can you please share a link to something that indicates why this would be a
good tool for modeling such experimental pulling scenarios? Making the case
for implementing such a feature would benefit from that.

Mark
> 
>



*This is our response *


Dear Mark,

There are several experiments have been done for protein and DNA unfolding.
Thy  became pioneer in this field.  That is why force should apply and
corresponding reaction
coordinates are measured . Here Gromacs login do not allow to upload larger
data.
But I can mention some paper address . If get time Please go through these
papers .

1- NATURE | VOL 421 | 23 JANUARY 2003 | www.nature.com/nature (Carlos
Bustamante*†, Zev Bryant* & Steven B. Smith†)

2-  SCIENCE 1⁄7 VOL. 275 1⁄7 28 FEBRUARY 1997 (Matthias Rief, Filipp
Oesterhelt, Berthold Heymann,Hermann E. Gaub )

That is  why I  asked about force-extension protocol.  In Umbrella sampling
distance is increases linearly with the time and corresponding
force experienced by the system writes .

We still don't no that force/time which writes in .xvg file corresponds
which formula like f= k(vt-x) or something else.
There are other lot experiments regarding measurement of stability of the
DNA and protein under f/x curve.
One can see some theory paper also to see f/x like.

1- THE JOURNAL OF CHEMICAL PHYSICS 148, 215105 (2018)




Note- According to Justin one  can write that protocol. If suppose we write
that protocol, then how  to apply in gromacs.

There are only input .mdp files. We didn't know  where to built the force
subroutine in .ff (force field ) directory. or somewhere else.


Hoping for  response.






On Fri, Aug 31, 2018 at 6:08 PM, Rakesh Mishra  wrote:

> Dear  mark
> I had already discussed regarding force/extension protocol.
> But I didn't get any response from your side. I dont have
> idea to upload some pictures.
>
> On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> The list cannot accept attachments. Upload to a file sharing service and
>> share a link. We will likely need more background information also.
>>
>> Mark
>>
>> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:
>>
>> > Hi every body
>> > can any one  explain what is the mean of this graph
>> > obtained from gromacs  constant velocity pulling of dsDNA
>> > along the helical direction. (force.xvg). Basically sudden drop of force
>> > represents what ?
>> > --
>> > 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.
>> --
>> 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.
>>
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491, +918777496532*
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
-- 
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Re: [gmx-users] (no subject)

[Rakesh Mishra]

Dear  mark
I had already discussed regarding force/extension protocol.
But I didn't get any response from your side. I dont have
idea to upload some pictures.

On Fri, Aug 31, 2018 at 4:05 PM, Mark Abraham 
wrote:

> Hi,
>
> The list cannot accept attachments. Upload to a file sharing service and
> share a link. We will likely need more background information also.
>
> Mark
>
> On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:
>
> > Hi every body
> > can any one  explain what is the mean of this graph
> > obtained from gromacs  constant velocity pulling of dsDNA
> > along the helical direction. (force.xvg). Basically sudden drop of force
> > represents what ?
> > --
> > 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.
> --
> 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.
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
-- 
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

The list cannot accept attachments. Upload to a file sharing service and
share a link. We will likely need more background information also.

Mark

On Fri, Aug 31, 2018, 12:22 Rakesh Mishra  wrote:

> Hi every body
> can any one  explain what is the mean of this graph
> obtained from gromacs  constant velocity pulling of dsDNA
> along the helical direction. (force.xvg). Basically sudden drop of force
> represents what ?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] (no subject)

[Soham Sarkar]

No I didn't try it. Its a nice idea.. I will try it.

On Sun, Jul 22, 2018 at 3:28 AM  wrote:

> Have you tried the  "insert-chemicals-after-md" command ?
>
> PB
>
> > On Jul 11, 2018, at 4:50 AM, Mark Abraham 
> wrote:
> >
> > Hi,
> >
> > Are you trying to observe something about the transition, or merely the
> > different end points?
> >
> > Mark
> >
> >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar 
> wrote:
> >>
> >> Dear all,
> >> I am planning to do a simulation where after 50ns of simulation I want
> to
> >> add some other chemicals in the system and continue it for another
> 50ns, so
> >> that I can have the effect of that chemicals exclusively before and
> after
> >> adding it to the system.Is it at all possible? If yes please tell me the
> >> protocol/ commands or give me some references where this type of
> simulation
> >> is used. Thanks in advance.
> >> -Soham
> >> --
> >> 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.
> >>
> > --
> > 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.
>
> --
> 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.
>


-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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Re: [gmx-users] (no subject)

[pbuscemi]

Have you tried the  "insert-chemicals-after-md" command ?

PB

> On Jul 11, 2018, at 4:50 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> Are you trying to observe something about the transition, or merely the
> different end points?
> 
> Mark
> 
>> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar  wrote:
>> 
>> Dear all,
>> I am planning to do a simulation where after 50ns of simulation I want to
>> add some other chemicals in the system and continue it for another 50ns, so
>> that I can have the effect of that chemicals exclusively before and after
>> adding it to the system.Is it at all possible? If yes please tell me the
>> protocol/ commands or give me some references where this type of simulation
>> is used. Thanks in advance.
>> -Soham
>> --
>> 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.
>> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

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Re: [gmx-users] (no subject)

[Soham Sarkar]

Thanks a lot..

On Sat, 21 Jul 2018, 9:57 pm Mark Abraham,  wrote:

> Hi,
>
> If you want to see whether a helix forms in a given solution, start from a
> random coil in that solution. Don't start from a helix in another solution.
>
> Marm
>
> On Sat, Jul 21, 2018, 17:41 Soham Sarkar  wrote:
>
> > Dear Mark,
> > I cant properly get your reply.. If you could elaborate it, it would be
> > nice
> > - Soham
> >
> > On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, 
> > wrote:
> >
> > > Hi,
> > >
> > > Then all you need is the starting point for potential helix formation.
> > You
> > > don't need to see it unravel.
> > >
> > > Mark
> > >
> > > On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
> > >
> > > > I want to see the helix transition.. whether it is coming back or not
> > in
> > > > the presence of the protecting osmolyte where urea is already there
> in
> > > the
> > > > system
> > > >
> > > > On Sat, 21 Jul 2018, 2:21 am Mark Abraham,  >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You haven't answered the question clearly. Do you care about
> > observing
> > > > the
> > > > > transition (whose properties will depend on how you introduce the
> > > > mixing),
> > > > > or just the difference between before and after? Your proposed
> method
> > > is
> > > > > ill formed because you can't continue a simulation after
> > fundamentally
> > > > > changing its composition. If you were watching a circus juggler
> > keeping
> > > > > five balls in the air, froze time and added two knives to the items
> > in
> > > > the
> > > > > air, it's not going to be consistent with any pattern in which a
> set
> > of
> > > > > five balls and two knives can be juggled.
> > > > >
> > > > > Mark
> > > > >
> > > > >
> > > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar 
> > wrote:
> > > > >
> > > > > > Dear Mark,
> > > > > > Sorry for late reply of your queries. Frankly speaking I am
> > planning
> > > to
> > > > > run
> > > > > > a REMD for 50ns with protein urea and water in it, then after
> 50ns
> > I
> > > > want
> > > > > > to add a protecting osmolyte into the system and want to continue
> > it
> > > > for
> > > > > > another 50ns REMD so that I can have the effect of the protecting
> > > > > osmolyte
> > > > > > before and after adding it into the system. My question is, what
> I
> > > have
> > > > > > planned is at all possible? How do I continue the simulation of
> > 50ns
> > > > for
> > > > > > another 50ns with a protecting osmolyte in it. Is there any
> > > references
> > > > or
> > > > > > commnad lines or protocols to execute this type of simulation
> which
> > > is
> > > > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > > > Thanks in advance.
> > > > > > - Soham
> > > > > >
> > > > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > > > wrote:
> > > > > >
> > > > > > > Dear all,
> > > > > > >  I am planning to do a simulation where after 50ns of
> simulation
> > I
> > > > want
> > > > > > to
> > > > > > > add some other chemicals in the system and continue it for
> > another
> > > > > 50ns,
> > > > > > so
> > > > > > > that I can have the effect of that chemicals exclusively before
> > and
> > > > > after
> > > > > > > adding it to the system.Is it at all possible? If yes please
> tell
> > > me
> > > > > the
> > > > > > > protocol/ commands or give me some references where this type
> of
> > > > > > simulation
> > > > > > > is used. Thanks in advance.
> > > > > > > -Soham
> > > > > > >
> > > > > > --
> > > > > > 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.
> > > > > >
> > > > > --
> > > > > 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.
> > > > >
> > > > --
> > > > 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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> > > >
> > > > * 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.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please 

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

If you want to see whether a helix forms in a given solution, start from a
random coil in that solution. Don't start from a helix in another solution.

Marm

On Sat, Jul 21, 2018, 17:41 Soham Sarkar  wrote:

> Dear Mark,
> I cant properly get your reply.. If you could elaborate it, it would be
> nice
> - Soham
>
> On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > Then all you need is the starting point for potential helix formation.
> You
> > don't need to see it unravel.
> >
> > Mark
> >
> > On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
> >
> > > I want to see the helix transition.. whether it is coming back or not
> in
> > > the presence of the protecting osmolyte where urea is already there in
> > the
> > > system
> > >
> > > On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > You haven't answered the question clearly. Do you care about
> observing
> > > the
> > > > transition (whose properties will depend on how you introduce the
> > > mixing),
> > > > or just the difference between before and after? Your proposed method
> > is
> > > > ill formed because you can't continue a simulation after
> fundamentally
> > > > changing its composition. If you were watching a circus juggler
> keeping
> > > > five balls in the air, froze time and added two knives to the items
> in
> > > the
> > > > air, it's not going to be consistent with any pattern in which a set
> of
> > > > five balls and two knives can be juggled.
> > > >
> > > > Mark
> > > >
> > > >
> > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar 
> wrote:
> > > >
> > > > > Dear Mark,
> > > > > Sorry for late reply of your queries. Frankly speaking I am
> planning
> > to
> > > > run
> > > > > a REMD for 50ns with protein urea and water in it, then after 50ns
> I
> > > want
> > > > > to add a protecting osmolyte into the system and want to continue
> it
> > > for
> > > > > another 50ns REMD so that I can have the effect of the protecting
> > > > osmolyte
> > > > > before and after adding it into the system. My question is, what I
> > have
> > > > > planned is at all possible? How do I continue the simulation of
> 50ns
> > > for
> > > > > another 50ns with a protecting osmolyte in it. Is there any
> > references
> > > or
> > > > > commnad lines or protocols to execute this type of simulation which
> > is
> > > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > > Thanks in advance.
> > > > > - Soham
> > > > >
> > > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > > wrote:
> > > > >
> > > > > > Dear all,
> > > > > >  I am planning to do a simulation where after 50ns of simulation
> I
> > > want
> > > > > to
> > > > > > add some other chemicals in the system and continue it for
> another
> > > > 50ns,
> > > > > so
> > > > > > that I can have the effect of that chemicals exclusively before
> and
> > > > after
> > > > > > adding it to the system.Is it at all possible? If yes please tell
> > me
> > > > the
> > > > > > protocol/ commands or give me some references where this type of
> > > > > simulation
> > > > > > is used. Thanks in advance.
> > > > > > -Soham
> > > > > >
> > > > > --
> > > > > 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.
> > > > >
> > > > --
> > > > 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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> > --
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> >
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Re: [gmx-users] (no subject)

[Soham Sarkar]

Dear Mark,
I cant properly get your reply.. If you could elaborate it, it would be nice
- Soham

On Sat, 21 Jul 2018, 8:47 pm Mark Abraham,  wrote:

> Hi,
>
> Then all you need is the starting point for potential helix formation. You
> don't need to see it unravel.
>
> Mark
>
> On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
>
> > I want to see the helix transition.. whether it is coming back or not in
> > the presence of the protecting osmolyte where urea is already there in
> the
> > system
> >
> > On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> > wrote:
> >
> > > Hi,
> > >
> > > You haven't answered the question clearly. Do you care about observing
> > the
> > > transition (whose properties will depend on how you introduce the
> > mixing),
> > > or just the difference between before and after? Your proposed method
> is
> > > ill formed because you can't continue a simulation after fundamentally
> > > changing its composition. If you were watching a circus juggler keeping
> > > five balls in the air, froze time and added two knives to the items in
> > the
> > > air, it's not going to be consistent with any pattern in which a set of
> > > five balls and two knives can be juggled.
> > >
> > > Mark
> > >
> > >
> > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:
> > >
> > > > Dear Mark,
> > > > Sorry for late reply of your queries. Frankly speaking I am planning
> to
> > > run
> > > > a REMD for 50ns with protein urea and water in it, then after 50ns I
> > want
> > > > to add a protecting osmolyte into the system and want to continue it
> > for
> > > > another 50ns REMD so that I can have the effect of the protecting
> > > osmolyte
> > > > before and after adding it into the system. My question is, what I
> have
> > > > planned is at all possible? How do I continue the simulation of 50ns
> > for
> > > > another 50ns with a protecting osmolyte in it. Is there any
> references
> > or
> > > > commnad lines or protocols to execute this type of simulation which
> is
> > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > Thanks in advance.
> > > > - Soham
> > > >
> > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > wrote:
> > > >
> > > > > Dear all,
> > > > >  I am planning to do a simulation where after 50ns of simulation I
> > want
> > > > to
> > > > > add some other chemicals in the system and continue it for another
> > > 50ns,
> > > > so
> > > > > that I can have the effect of that chemicals exclusively before and
> > > after
> > > > > adding it to the system.Is it at all possible? If yes please tell
> me
> > > the
> > > > > protocol/ commands or give me some references where this type of
> > > > simulation
> > > > > is used. Thanks in advance.
> > > > > -Soham
> > > > >
> > > > --
> > > > 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.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
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> > > 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] (no subject)

[Mark Abraham]

Hi,

Then all you need is the starting point for potential helix formation. You
don't need to see it unravel.

Mark

On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:

> I want to see the helix transition.. whether it is coming back or not in
> the presence of the protecting osmolyte where urea is already there in the
> system
>
> On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > You haven't answered the question clearly. Do you care about observing
> the
> > transition (whose properties will depend on how you introduce the
> mixing),
> > or just the difference between before and after? Your proposed method is
> > ill formed because you can't continue a simulation after fundamentally
> > changing its composition. If you were watching a circus juggler keeping
> > five balls in the air, froze time and added two knives to the items in
> the
> > air, it's not going to be consistent with any pattern in which a set of
> > five balls and two knives can be juggled.
> >
> > Mark
> >
> >
> > On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:
> >
> > > Dear Mark,
> > > Sorry for late reply of your queries. Frankly speaking I am planning to
> > run
> > > a REMD for 50ns with protein urea and water in it, then after 50ns I
> want
> > > to add a protecting osmolyte into the system and want to continue it
> for
> > > another 50ns REMD so that I can have the effect of the protecting
> > osmolyte
> > > before and after adding it into the system. My question is, what I have
> > > planned is at all possible? How do I continue the simulation of 50ns
> for
> > > another 50ns with a protecting osmolyte in it. Is there any references
> or
> > > commnad lines or protocols to execute this type of simulation which is
> > > exclusively dedicated to the effect of a chemicals in the system.
> > > Thanks in advance.
> > > - Soham
> > >
> > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> wrote:
> > >
> > > > Dear all,
> > > >  I am planning to do a simulation where after 50ns of simulation I
> want
> > > to
> > > > add some other chemicals in the system and continue it for another
> > 50ns,
> > > so
> > > > that I can have the effect of that chemicals exclusively before and
> > after
> > > > adding it to the system.Is it at all possible? If yes please tell me
> > the
> > > > protocol/ commands or give me some references where this type of
> > > simulation
> > > > is used. Thanks in advance.
> > > > -Soham
> > > >
> > > --
> > > 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.
> > >
> > --
> > 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] (no subject)

[Soham Sarkar]

I want to see the helix transition.. whether it is coming back or not in
the presence of the protecting osmolyte where urea is already there in the
system

On Sat, 21 Jul 2018, 2:21 am Mark Abraham,  wrote:

> Hi,
>
> You haven't answered the question clearly. Do you care about observing the
> transition (whose properties will depend on how you introduce the mixing),
> or just the difference between before and after? Your proposed method is
> ill formed because you can't continue a simulation after fundamentally
> changing its composition. If you were watching a circus juggler keeping
> five balls in the air, froze time and added two knives to the items in the
> air, it's not going to be consistent with any pattern in which a set of
> five balls and two knives can be juggled.
>
> Mark
>
>
> On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:
>
> > Dear Mark,
> > Sorry for late reply of your queries. Frankly speaking I am planning to
> run
> > a REMD for 50ns with protein urea and water in it, then after 50ns I want
> > to add a protecting osmolyte into the system and want to continue it for
> > another 50ns REMD so that I can have the effect of the protecting
> osmolyte
> > before and after adding it into the system. My question is, what I have
> > planned is at all possible? How do I continue the simulation of 50ns for
> > another 50ns with a protecting osmolyte in it. Is there any references or
> > commnad lines or protocols to execute this type of simulation which is
> > exclusively dedicated to the effect of a chemicals in the system.
> > Thanks in advance.
> > - Soham
> >
> > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar,  wrote:
> >
> > > Dear all,
> > >  I am planning to do a simulation where after 50ns of simulation I want
> > to
> > > add some other chemicals in the system and continue it for another
> 50ns,
> > so
> > > that I can have the effect of that chemicals exclusively before and
> after
> > > adding it to the system.Is it at all possible? If yes please tell me
> the
> > > protocol/ commands or give me some references where this type of
> > simulation
> > > is used. Thanks in advance.
> > > -Soham
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

You haven't answered the question clearly. Do you care about observing the
transition (whose properties will depend on how you introduce the mixing),
or just the difference between before and after? Your proposed method is
ill formed because you can't continue a simulation after fundamentally
changing its composition. If you were watching a circus juggler keeping
five balls in the air, froze time and added two knives to the items in the
air, it's not going to be consistent with any pattern in which a set of
five balls and two knives can be juggled.

Mark


On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:

> Dear Mark,
> Sorry for late reply of your queries. Frankly speaking I am planning to run
> a REMD for 50ns with protein urea and water in it, then after 50ns I want
> to add a protecting osmolyte into the system and want to continue it for
> another 50ns REMD so that I can have the effect of the protecting osmolyte
> before and after adding it into the system. My question is, what I have
> planned is at all possible? How do I continue the simulation of 50ns for
> another 50ns with a protecting osmolyte in it. Is there any references or
> commnad lines or protocols to execute this type of simulation which is
> exclusively dedicated to the effect of a chemicals in the system.
> Thanks in advance.
> - Soham
>
> On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar,  wrote:
>
> > Dear all,
> >  I am planning to do a simulation where after 50ns of simulation I want
> to
> > add some other chemicals in the system and continue it for another 50ns,
> so
> > that I can have the effect of that chemicals exclusively before and after
> > adding it to the system.Is it at all possible? If yes please tell me the
> > protocol/ commands or give me some references where this type of
> simulation
> > is used. Thanks in advance.
> > -Soham
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] (no subject)

[Soham Sarkar]

Dear Krieger,
Frankly speaking I am planning to run a REMD for 50ns with protein urea and
water in it, then after 50ns I want to add a protecting osmolyte into the
system and want to continue it for another 50ns REMD so that I can have the
effect of the protecting osmolyte before and after adding it into the
system. My question is, what I have planned is at all possible? How do I
continue the simulation of 50ns for another 50ns with a protecting osmolyte
in it. Is there any references or commnad lines or protocols to execute
this type of simulation which is exclusively dedicated to the effect of a
chemicals in the system.
Thanks in advance.
- Soham

On Tue, 10 Jul 2018, 4:51 pm Soham Sarkar,  wrote:

> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
>
-- 
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Re: [gmx-users] (no subject)

[Soham Sarkar]

Dear Mark,
Sorry for late reply of your queries. Frankly speaking I am planning to run
a REMD for 50ns with protein urea and water in it, then after 50ns I want
to add a protecting osmolyte into the system and want to continue it for
another 50ns REMD so that I can have the effect of the protecting osmolyte
before and after adding it into the system. My question is, what I have
planned is at all possible? How do I continue the simulation of 50ns for
another 50ns with a protecting osmolyte in it. Is there any references or
commnad lines or protocols to execute this type of simulation which is
exclusively dedicated to the effect of a chemicals in the system.
Thanks in advance.
- Soham

On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar,  wrote:

> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
>
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Re: [gmx-users] (no subject)

[James Krieger]

You can probably use gmx solvate for this with the frame at the end of 50
ns as input cp and a box of the new molecules as cs or possibly genion. We
also have a tool for building simulation systems with small molecules
called DruGUI http://prody.csb.pitt.edu/drugui/ although I don't know how
you would convert the topology from NAMD .psf to Gromacs .top format.

Best wishes
James

On Tue, Jul 10, 2018 at 7:21 AM, Soham Sarkar  wrote:

> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
> --
> 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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>
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Are you trying to observe something about the transition, or merely the
different end points?

Mark

On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar  wrote:

> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
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Re: [gmx-users] (no subject)

[Dallas Warren]

If you aren't adding anything too big, or to much of them, then take
the final frame, use gmx insert-molecules (probably with a reduced vdw
radius so they fit in) to put the additional molecule(s) in, perform
standard pre production run energy minimisation etc, then off it goes
again.

Why can't you start two separate systems, one without, and one with?
That would be a more robust way to do it.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 10 Jul 2018 at 21:22, Soham Sarkar  wrote:
>
> Dear all,
>  I am planning to do a simulation where after 50ns of simulation I want to
> add some other chemicals in the system and continue it for another 50ns, so
> that I can have the effect of that chemicals exclusively before and after
> adding it to the system.Is it at all possible? If yes please tell me the
> protocol/ commands or give me some references where this type of simulation
> is used. Thanks in advance.
> -Soham
> --
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Re: [gmx-users] (no subject)

[Vytautas Rakeviius]

 
Also depends on what you try to do. Maybe Dry Martini? Look into:ARNAREZ, 
Clément, et al. Dry Martini, a coarse-grained force field for lipid membrane 
simulations with implicit solvent. Journal of chemical theory and computation, 
2014, 11.1: 260-275.
On Thursday, June 21, 2018, 5:22:15 AM GMT+3, Chhaya Singh 
 wrote:  
 
 I want to perform MD simulation using groamcs in implicit solvent. Can you
help me which force field is compatible with which solvent I can take?
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Re: [gmx-users] (no subject)

[Srijan Singh]

Thank you,
it worked.

On Mon, May 14, 2018 at 3:43 PM, Mark Abraham 
wrote:

> Hi,
>
> I don't know whether solvate supports such boxes, but if it does I would
> use editconf first to describe the box, and then solvate to fill it.
> Currently you are filling a cubic box and then transforming it to another
> shape, and that isn't a well formed operation.
>
> Mark
>
> On Mon, May 14, 2018 at 7:49 AM Srijan Singh 
> wrote:
>
> > Hello all,
> >
> > I modeled a hexagonal box of water using the following steps:
> >
> > gmx solvate -cs spc216.gro -o waterst1 -box 6 6 6
> >
> > gmx editconf -f waterst1.gro -o w120.gro -bt tric -box 4.5 4.5 5.56
> -angles
> > 90 90 120 -c
> >
> > After which i used trjconv with -pbc atom -ur compact and obtained the
> > hexagonal cylinder.
> >
> > But while minimizing the system , i encountered large forces (due to
> > overlapping atoms )  and on deleting(the overlapped molecule) and
> > minimizing the same thing happened again.
> >
> > when i ran equlibriation instead of minimization (after deleting
> overlapped
> > molecule), it too crashed.
> >
> > I'm using tip3p water with opls forcefield.
> > I am attaching the topology files and mdp file file for minimization
> below.
> > I am relatively new to gromacs so if anyone could please point out any
> > error which i'm making.
> >
> > Thanks in advance
> > Srijan
> > --
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

I don't know whether solvate supports such boxes, but if it does I would
use editconf first to describe the box, and then solvate to fill it.
Currently you are filling a cubic box and then transforming it to another
shape, and that isn't a well formed operation.

Mark

On Mon, May 14, 2018 at 7:49 AM Srijan Singh  wrote:

> Hello all,
>
> I modeled a hexagonal box of water using the following steps:
>
> gmx solvate -cs spc216.gro -o waterst1 -box 6 6 6
>
> gmx editconf -f waterst1.gro -o w120.gro -bt tric -box 4.5 4.5 5.56 -angles
> 90 90 120 -c
>
> After which i used trjconv with -pbc atom -ur compact and obtained the
> hexagonal cylinder.
>
> But while minimizing the system , i encountered large forces (due to
> overlapping atoms )  and on deleting(the overlapped molecule) and
> minimizing the same thing happened again.
>
> when i ran equlibriation instead of minimization (after deleting overlapped
> molecule), it too crashed.
>
> I'm using tip3p water with opls forcefield.
> I am attaching the topology files and mdp file file for minimization below.
> I am relatively new to gromacs so if anyone could please point out any
> error which i'm making.
>
> Thanks in advance
> Srijan
> --
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 4/23/18 5:08 PM, rose rahmani wrote:

Hi,

I have a capped amino acid in box of water and ion(but the system is not
charged) and named it initial.gro, i can see some unreal bonds when i open
it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H
atom where nonbobded and were single atoms around remained bonded
structure.( maybe aminoacid in initial.gro file didn't get well optimized
or anything... )

But when i run nvt, the amino acid structure get real structure and
everything is ok.

I remember Justin said that MD and GROMACS can't make or break bond. So
What happend to my system?


You had lousy initial coordinates, which showed up as a badly distorted 
geometry. It should look normal after energy minimization (which it 
probably did, otherwise NVT equilibration never would have worked).


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Either your topology components are in the wrong order (like the message
says) or you're doing something strange. Notice how your water won't have
any atoms unless _FF_CHARMM is defined, which will only be defined if
you've got a charmm force field involved. But nobody's got enough
information to help you.

And please do yourself a favour and get a more recent GROMACS version
installed. It's been more than 7 years since 4.5.5...

Mark

‪On Wed, Jan 24, 2018 at 10:45 AM ‫حلیمه میرسالاری‬‎ <
h.mirsalar...@gmail.com> wrote:‬

> Dear all
>
> l am using gromacs 4.5.5 version for simulation carbon nanotubes  with
> charmm27 force feild ,there was no error grompp stage,but when l do
> simulation of carbon nanotube in tip3p  water encountered with
>  fatal error:
>
>   [ file tip3p.itp, line 40]:
> Atom index (1) in settles out of bounds (1-0).
> This probably means that you have inserted topology section "settles"
> in a part belonging to a different molecule than you intended to.
> In that case move the "settles" section to the right molecule.
>
> Please guide me
>
> File:tip3p.itp
>
> Thanks
>
> Halimeh
>
>
>  1
>  2
>  3
>  4
>  5
>  6
>  7
>  8
>  9
> 10
> 11
> 12
> 13
> 14
> 15
> 16
> 17
> 18
> 19
> 20
> 21
> 22
> 23
> 24
> 25
> 26
> 27
> 28
> 29
> 30
> 31
> 32
> 33
> 34
> 35
> 36
> 37
> 38
> 39
> 40
> 41
> 42
> 43
> 44
> 45
> 46
>
> [ moleculetype ]
> ; molname  nrexcl
> SOL 2
>
> [ atoms ]
> ; id   at type  res nr  residu name at name cg nr   charge
> #ifdef _FF_CHARMM
> 1   OWT31   SOL  OW 1   -0.834
> 2   HWT31   SOL HW1 10.417
> 3   HWT31   SOL HW2 10.417
> #endif
>
>
> #ifdef FLEXIBLE
>
> #ifdef CHARMM_TIP3P
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 376560.0 0.09572376560.0
> 1   3   1   0.09572 376560.0 0.09572376560.0
>
> [ angles ]
> ; i  j  k   funct   angle   force.c.
> 21  3   1   104.52  460.24  104.52  460.24
> #else
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 502416.0 0.09572502416.0
> 1   3   1   0.09572 502416.0 0.09572502416.0
>
> [ angles ]
> ; i  j  k   funct   angle   force.c.
> 21  3   1   104.52  628.02  104.52  628.02
> #endif
>
>
> #else
> [ settles ]
> ; i   j funct   length
> 1 1 0.09572 0.15139
>
> [ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
> #endif
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Re: [gmx-users] (no subject)

[João Henriques]

> You need some ions to neutralise the system for long range electrostatics
to work.

This mostly applies to PME. However, because PME is basically *de
facto* nowadays,
it will most likely apply in most situations. However, I recently learned
that PME can also be run with a non-neutral system, as PME will introduce a
neutralizing background charge (and dipole corrections). Here is the
thread:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg29536.html

> We usually add more to make the simulation more like the real system
(solution or cell).

Just to be the devil's advocate, I'd say that based on anecdotal evidence
adding salt in a MD simulation of a protein changes make little to no
difference. It doesn't behave as expected, most likely due to poor ion
parametrization and integer charges.

J


On Sun, Jan 21, 2018 at 7:16 AM,  wrote:

> You need some ions to neutralise the system for long range electrostatics
> to work. We usually add more to make the simulation more like the real
> system (solution or cell).
>
> > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in>
> wrote:
> >
> > Dear all,
> >
> >I am a beginer. I would like to know the purpose of adding
> ions
> > during the simulation process.
> > --
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Re: [gmx-users] (no subject)

[jamesmkrieger]

You need some ions to neutralise the system for long range electrostatics to 
work. We usually add more to make the simulation more like the real system 
(solution or cell).

> On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in> wrote:
> 
> Dear all,
> 
>I am a beginer. I would like to know the purpose of adding ions
> during the simulation process.
> -- 
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Re: [gmx-users] (no subject)

[Alex]

A beginner in what? Your question has nothing to do with Gromacs.

Alex


On 1/20/2018 11:12 PM, Sankaran SV . wrote:

Dear all,

 I am a beginer. I would like to know the purpose of adding ions
during the simulation process.


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Re: [gmx-users] (no subject)

[Rakesh Mishra]

Thanks Justin

I followed your suggestion. now I am able to restrain (immobile) any
molecule during pulling.

thanks for your help.

On Tue, Jan 2, 2018 at 4:56 PM, Rakesh Mishra  wrote:

> Dear all
>
> I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I
> am doing  pulling for si-rna  (double stranded, 22 nucleotides each ). I
> am applying
> pulling code of  umbrella sampling. Using that, we have chosen 22nd number
> residue of chain A is under pulling with constant velocity rate in +ve x
> direction.  and residue 44 of  apposite chain B at the apposite end is
> taking as reference . Now I am thinking to make the reference residue 44 as
> immobile. But when
> after simulation I am trying to see the trajectory . Then I Am finding that
> the residue n 44 (reference residue of pulling) is also moving and which is
> in apposite direction.
> even it is showing that reference residue 44 is crossing the box wall in
> -ve x direction.
>
> My aim is to pull residue n 22 of chain-A of si-rna by making reference
> residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
> motion in apposite direction.
>
> --
> * Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491 <094736%2062491>, +91877749632*
>



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
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Re: [gmx-users] (no subject)

[Vytautas Rakeviius]

You should give more details how you try to make residue 44 immobile. Keep in 
mind that some ways to do that can be "defeated" with strong enough pulling. 
Most likely you just have to try few times with different pulling and 
restraining options.
 

On Tuesday, January 2, 2018, 12:30:59 PM GMT+2, Rakesh Mishra 
 wrote:  
 
 Dear sir

I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I
am doing
 pulling for si-rna  (double stranded, 22 nucleotides each ). I am applying
pulling code of  umbrella sampling. Using that, we have chosen 22nd number
residue of chain A is under pulling with constant velocity rate in +ve x
direction.  and residue 44 of  apposite chain B at the apposite end is
taking as reference . Now I am thinking to make the reference residue 44 as
immobile. But when
after simulation I am trying to see the trajectory . Then I Am finding that
the residue n 44 (reference residue of pulling) is also moving and which is
in apposite direction.
even it is showing that reference residue 44 is crossing the box wall in
-ve x direction.

My aim is to pull residue n 22 of chain-A of si-rna by making reference
residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
motion in apposite direction.

-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 1/2/18 6:26 AM, Rakesh Mishra wrote:

Dear all

I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I


If you're just starting out, don't use outdated software. Use the latest 
official version (2016.4) and be ready for a brand new 2018 release 
sometime soon.



am doing  pulling for si-rna  (double stranded, 22 nucleotides each ). I am
applying
pulling code of  umbrella sampling. Using that, we have chosen 22nd number
residue of chain A is under pulling with constant velocity rate in +ve x
direction.  and residue 44 of  apposite chain B at the apposite end is
taking as reference . Now I am thinking to make the reference residue 44 as
immobile. But when
after simulation I am trying to see the trajectory . Then I Am finding that
the residue n 44 (reference residue of pulling) is also moving and which is
in apposite direction.
even it is showing that reference residue 44 is crossing the box wall in
-ve x direction.


There is nothing wrong with this. For every action, there is an equal 
but opposite reaction, after all.



My aim is to pull residue n 22 of chain-A of si-rna by making reference
residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
motion in apposite direction.



If you want an immobile reference for whatever reason, apply position 
restraints to residue 44. You'll need to create a custom restraint file 
with genrestr and a suitable index group, or by hand.


-Justin

--
==

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

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

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

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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 10/27/17 5:51 AM, saranya wrote:

Dear Users,
I have done a simulation of Aggregated amyloid beta peptide for 100ns. The
pdb structure choosen for my work is 1IYT, which has several (10) model
structures, but i have choosen only 4 structure for my simulation. The
problem is after production, if i check the final .gro files of md instead
of 4 peptide structure i got only a single peptide structure. What is the
reason for getting this result?


You can only simulate a single structure at one time. If you chose 4 
structures, presumably you ran 4 different simulations and obtained 4 
different trajectories and final configurations, correct?


-Justin

--
==

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

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

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

==

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Re: [gmx-users] (no subject)

[R C Dash]

use trjconv command with nojump option to center all the peptide. Use the
starting structure as the starting configuration.

regards,
RC Dash

On Fri, Oct 27, 2017 at 5:51 AM, saranya  wrote:

> Dear Users,
> I have done a simulation of Aggregated amyloid beta peptide for 100ns. The
> pdb structure choosen for my work is 1IYT, which has several (10) model
> structures, but i have choosen only 4 structure for my simulation. The
> problem is after production, if i check the final .gro files of md instead
> of 4 peptide structure i got only a single peptide structure. What is the
> reason for getting this result?
>
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Thanks for the answering
I have doubts , because in the gromacs manual , they have mentioned that ,
the application of Essential dynamics is also to enhance the sampling with
respect to usual MD. So, i want to make sure whether my understanding about
ED is correct or not ?


On Oct 19, 2017 5:46 AM, "Dallas Warren"  wrote:

> Essential Dynamics = extracts the correlated motions of proteins to
> understand the motions that are most fundamental to the activity of
> the protein (http://www.gromacs.org/Documentation/How-tos/
> Essential_Dynamics)
> Accelerated MD = enhanced-sampling method that improves the
> conformational space sampling by reducing energy barriers separating
> different states of a system
> (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html)
>
> Found via a quick search.
>
> From those quick definitions, they do two different things.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 17 October 2017 at 21:16, Kingsley Theras Primus Dass .
> <105726...@gms.tcu.edu.tw> wrote:
> > Hi all,
> > I have a very basic question about essential dynamics. I want to know
> > whether essential dynamics function is similar to Accelerated MD ? Or
> > essential dynamics is different from Accelerated MD ?
> >
> > Thanks in advance.
> >
> > Kingsleg Theras
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 10/19/17 11:30 AM, Robert Nairn wrote:

Yes I noticed the area per protein was displaying 0 from the output on the
terminal.

Having repeated the tutorial with my protein, i consistently get two
messages that could be responsible. If i try to select start terminus as
none (2) as per the tutorial I receive a message saying:


The tutorial chooses no terminal patching because I already built on 
capping groups (acetyl and amide) to both termini. If this is not the 
case in your system, it's not an appropriate choice.



Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
 MET1  MET126  MET251  MET376
  SD5   SD956  SD1907  SD2858
   MET126   SD956   3.533
   MET251  SD1907   5.410   3.187
   MET376  SD2858   5.451   5.516   3.535
   MET501  SD3809   3.427   5.522   5.366   3.172
Select start terminus type for MET-1
  0: NH3+
  1: NH2
  2: None
2
Start terminus MET-1: None
Select end terminus type for ASN-625
  0: COO-
  1: COOH
  2: None
2
End terminus ASN-625: None

---
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1088

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Alternatively I've used uncharged terminal end (1) for NH2 and COOH and get
this warning:


Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
 MET1  MET126  MET251  MET376
  SD5   SD956  SD1907  SD2858
   MET126   SD956   3.533
   MET251  SD1907   5.410   3.187
   MET376  SD2858   5.451   5.516   3.535
   MET501  SD3809   3.427   5.522   5.366   3.172
Select start terminus type for MET-1
  0: NH3+
  1: NH2
  2: None
1
Start terminus MET-1: NH2
Select end terminus type for ASN-625
  0: COO-
  1: COOH
  2: None
1
End terminus ASN-625: COOH


That's chemically impossible but at least it's a syntactically correct 
choice.



Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 625 residues with 6003 atoms
Making bonds...
Warning: Long Bond (1200-1202 = 5.44802 nm)
Warning: Long Bond (2400-2402 = 5.45768 nm)
Warning: Long Bond (3600-3602 = 5.21815 nm)
Warning: Long Bond (4800-4802 = 5.51416 nm)
Number of bonds was 6071, now 6067
Generating angles, dihedrals and pairs...
Don't ignore these - they mean you probably have missing residues in the 
structure.


I'm not sure any of the above is in any way related to the InflateGRO 
failure (and really, without the coordinate file itself, there's not 
much to go on) but you have plenty to consider about how reasonable your 
starting system is.


-Justin


WARNING: WARNING: Residue 1 named MET of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I've looked through the pdb input files and the .gro output files and can't
find and erroneous hydrogen atoms, I've also been sure to change all HW
atom types to H.

I'm unsure if this is where my problem lies...

Thanks,

Robert


On 19 October 2017 at 10:55, Justin Lemkul  wrote:



On 10/19/17 8:04 AM, Robert Nairn wrote:


Dear all,

I am currently trying to insert the MscL protein into the DMPC bilayer. I
followed Justin Lemkul's tutorial 2 (with the exception of using dmpc
instead of dppc) and receive this error message after shrinking and energy
minimization.


[christos@chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em
 :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:

  GROMACS is written by:
   Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
   Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
Fritsch
Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
Hindriksen
   Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
Kutzner
  Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
Meulenhoff
 Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
 Roland Schulz Alexey Shvetsov Michael Shirts Alfons
Sijbers
 Peter TielemanTeemu Virolainen  Christian 

Re: [gmx-users] (no subject)

[Robert Nairn]

Yes I noticed the area per protein was displaying 0 from the output on the
terminal.

Having repeated the tutorial with my protein, i consistently get two
messages that could be responsible. If i try to select start terminus as
none (2) as per the tutorial I receive a message saying:

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1  MET126  MET251  MET376
 SD5   SD956  SD1907  SD2858
  MET126   SD956   3.533
  MET251  SD1907   5.410   3.187
  MET376  SD2858   5.451   5.516   3.535
  MET501  SD3809   3.427   5.522   5.366   3.172
Select start terminus type for MET-1
 0: NH3+
 1: NH2
 2: None
2
Start terminus MET-1: None
Select end terminus type for ASN-625
 0: COO-
 1: COOH
 2: None
2
End terminus ASN-625: None

---
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/usr/local/gromacs-5.1.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1088

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Alternatively I've used uncharged terminal end (1) for NH2 and COOH and get
this warning:


Processing chain 1 (4756 atoms, 625 residues)
Identified residue MET1 as a starting terminus.
Identified residue ASN625 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1  MET126  MET251  MET376
 SD5   SD956  SD1907  SD2858
  MET126   SD956   3.533
  MET251  SD1907   5.410   3.187
  MET376  SD2858   5.451   5.516   3.535
  MET501  SD3809   3.427   5.522   5.366   3.172
Select start terminus type for MET-1
 0: NH3+
 1: NH2
 2: None
1
Start terminus MET-1: NH2
Select end terminus type for ASN-625
 0: COO-
 1: COOH
 2: None
1
End terminus ASN-625: COOH
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 625 residues with 6003 atoms
Making bonds...
Warning: Long Bond (1200-1202 = 5.44802 nm)
Warning: Long Bond (2400-2402 = 5.45768 nm)
Warning: Long Bond (3600-3602 = 5.21815 nm)
Warning: Long Bond (4800-4802 = 5.51416 nm)
Number of bonds was 6071, now 6067
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named MET of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I've looked through the pdb input files and the .gro output files and can't
find and erroneous hydrogen atoms, I've also been sure to change all HW
atom types to H.

I'm unsure if this is where my problem lies...

Thanks,

Robert


On 19 October 2017 at 10:55, Justin Lemkul  wrote:

>
>
> On 10/19/17 8:04 AM, Robert Nairn wrote:
>
>> Dear all,
>>
>> I am currently trying to insert the MscL protein into the DMPC bilayer. I
>> followed Justin Lemkul's tutorial 2 (with the exception of using dmpc
>> instead of dppc) and receive this error message after shrinking and energy
>> minimization.
>>
>>
>> [christos@chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em
>> :-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
>>
>>  GROMACS is written by:
>>   Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>   Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
>> Fritsch
>>Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
>> Hindriksen
>>   Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
>> Kutzner
>>  Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>> Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons
>> Sijbers
>> Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>> and the project leaders:
>>  Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; 

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 10/19/17 8:04 AM, Robert Nairn wrote:

Dear all,

I am currently trying to insert the MscL protein into the DMPC bilayer. I
followed Justin Lemkul's tutorial 2 (with the exception of using dmpc
instead of dppc) and receive this error message after shrinking and energy
minimization.


[christos@chpc-cp39 Simulation]$ gmx mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
   gmx mdrun -v -deffnm em


Back Off! I just backed up em.log to ./#em.log.7#

Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
   CPU info:
 Vendor: GenuineIntel
 Brand:  Intel(R) Core(TM) i5-4460  CPU @ 3.20GHz
 SIMD instructions most likely to fit this hardware: AVX2_256
 SIMD instructions selected at GROMACS compile time: AVX2_256

Reading file em.tpr, VERSION 5.1.4 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads


Back Off! I just backed up em.trr to ./#em.trr.7#

Back Off! I just backed up em.edr to ./#em.edr.7#

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot= -3.20786e+05 Fmax= 1.71766e+03, atom=
328
Step=2, Dmax= 5.0e-03 nm, Epot= -3.22206e+05 Fmax= 2.42847e+03, atom=
5581
Step=3, Dmax= 6.0e-03 nm, Epot= -3.22537e+05 Fmax= 5.33224e+03, atom=
5581
Step=4, Dmax= 7.2e-03 nm, Epot= -3.23803e+05 Fmax= 3.73628e+03, atom=
5581
Step=6, Dmax= 4.3e-03 nm, Epot= -3.24377e+05 Fmax= 1.77965e+03, atom=
5581
Step=7, Dmax= 5.2e-03 nm, Epot= -3.24696e+05 Fmax= 4.72325e+03, atom=
5581
Step=8, Dmax= 6.2e-03 nm, Epot= -3.25203e+05 Fmax= 3.21307e+03, atom=
5581
Step=   10, Dmax= 3.7e-03 nm, Epot= -3.25578e+05 Fmax= 1.53786e+03, atom=
5581
Step=   11, Dmax= 4.5e-03 nm, Epot= -3.25794e+05 Fmax= 4.19745e+03, atom=
5581
Step=   12, Dmax= 5.4e-03 nm, Epot= -3.26199e+05 Fmax= 2.65229e+03, atom=
5581
Step=   14, Dmax= 3.2e-03 nm, Epot= -3.26475e+05 Fmax= 1.44458e+03, atom=
5581
Step=   15, Dmax= 3.9e-03 nm, Epot= -3.26646e+05 Fmax= 3.51711e+03, atom=
889
Step=   16, Dmax= 4.6e-03 nm, Epot= -3.26945e+05 Fmax= 2.42357e+03, atom=
889
Step=   18, Dmax= 2.8e-03 nm, Epot= -3.27174e+05 Fmax= 1.16101e+03, atom=
889
Step=   19, Dmax= 3.3e-03 nm, Epot= -3.27357e+05 Fmax= 3.10626e+03, atom=
889
Step=   20, Dmax= 4.0e-03 nm, Epot= -3.27599e+05 Fmax= 2.04763e+03, atom=
889
Step=   21, Dmax= 4.8e-03 nm, Epot= -3.27618e+05 Fmax= 4.11224e+03, atom=
889
Step=   22, Dmax= 5.8e-03 nm, Epot= -3.27866e+05 Fmax= 3.29947e+03, atom=
889
Step=   24, Dmax= 3.5e-03 nm, Epot= -3.28131e+05 Fmax= 1.11942e+03, atom=
889
Step=   25, Dmax= 4.2e-03 nm, Epot= -3.28185e+05 Fmax= 4.23073e+03, atom=
889
Step=   26, Dmax= 5.0e-03 nm, Epot= -3.28509e+05 Fmax= 2.13723e+03, atom=
889
Step=   28, Dmax= 3.0e-03 nm, Epot= -3.28653e+05 Fmax= 1.71455e+03, atom=
889
Step=   29, Dmax= 3.6e-03 nm, Epot= -3.28732e+05 Fmax= 2.86474e+03, atom=
889
Step=   30, Dmax= 4.3e-03 nm, Epot= -3.28867e+05 Fmax= 2.67060e+03, atom=
889
Step=   31, Dmax= 5.2e-03 nm, Epot= -3.28877e+05 Fmax= 3.93851e+03, atom=
889
Step=   32, Dmax= 6.2e-03 nm, Epot= -3.28983e+05 Fmax= 4.01820e+03, atom=
889
Step=   34, Dmax= 3.7e-03 nm, Epot= -3.29290e+05 Fmax= 7.22653e+02, atom=
889

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.7#

Steepest Descents converged to Fmax < 1000 in 35 steps
Potential Energy  = -3.2929012e+05
Maximum force =  7.2265314e+02 on atom 889
Norm of force =  7.2922180e+01

NOTE: 20 % of the run time was spent in pair search,
   you might want to increase nstlist (this has 

Re: [gmx-users] (no subject)

[Dallas Warren]

Essential Dynamics = extracts the correlated motions of proteins to
understand the motions that are most fundamental to the activity of
the protein (http://www.gromacs.org/Documentation/How-tos/Essential_Dynamics)
Accelerated MD = enhanced-sampling method that improves the
conformational space sampling by reducing energy barriers separating
different states of a system
(http://www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html)

Found via a quick search.

>From those quick definitions, they do two different things.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 17 October 2017 at 21:16, Kingsley Theras Primus Dass .
<105726...@gms.tcu.edu.tw> wrote:
> Hi all,
> I have a very basic question about essential dynamics. I want to know
> whether essential dynamics function is similar to Accelerated MD ? Or
> essential dynamics is different from Accelerated MD ?
>
> Thanks in advance.
>
> Kingsleg Theras
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/8/17 5:43 AM, abir paul wrote:

hi,
I am very new to gromacs. I want to see phosphorylation effect on a
protein molecule. So I have phosphorylated my protein in charmm-gui server.
when i tried to generate .gro file by using pdb2gmx command line it gives
me following error :

   Fatal error:
  Residue 1 named GLY of a molecule in the input file was mapped
  to an entry in the topology database, but the atom N used in
  an interaction of type improper in that entry is not found in
the
  input file. Perhaps your atom and/or residue naming needs to be
  fixed.

How can I fixed this error. please help me.


CHARMM-GUI will build the whole system for you, including generating the 
GROMACS topology and input files.  There's no need to run anything 
through pdb2gmx.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] (no subject)

[RAHUL SURESH]

I suggest check for the appropriate binding pocket. See whether the ligand
relocates at some other point in protein or keep to stay away. Also check
for the quality of the topology generated.

On Wed, Aug 16, 2017 at 10:11 AM,  wrote:

> Hii Everyone
>
> I had performed a 100ns protein-ligand (docked complex) simulation with
> gromacs 5.1.4.
>
> The ligand in my case is hydrogen peroxide.
>
> I have removed the PBC effect and centered the protein.
>
> I have used the following commands:
>
> gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc
>
> gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc
>
> I am analyzing the average distance between the protein and the ligand. I
> am getting a value of 3.2nm which is too high.
>
> Also in the out_1.xtc, after 10ns itself the ligand is moving all around
> the protein.
>
> Unable to understand why its happening!!
>
> Please suggest.
>
> Thank You
>
> Regards
>
> Z. Hazarika
> Research Scholar
> Tezpur University
> Tezpur, India
>
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] (no subject)

[Dan Gil]

Hi Iman,

If I understand, you are planning on calculating the surface tension of
water?

To me, it seems odd that you would try to apply a surface-tension couple to
your system, and then calculate the surface tension.

Dan

On Thu, Aug 10, 2017 at 5:42 AM, Iman Ahmadabadi  wrote:

> Dear Users,
>
> I'm determining my .mdp file for NPT equilibration, but I don't know how to
> determine the ref_p section of mdp.
>
> pcoupl = berendsen
> pcoupltype = surface-tension
> tau_p = 0.5 0.5
> ref_p = 1.0 1.0
> compressibility = 4.46e-5 4.46e-5
>
> I'm gonna to calculate surface tension for a layer of water.
>
> Sincerely,
> Iman
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Re: [gmx-users] (no subject)

[saranya]

There is a minimum number of hydrogen bond formation (2 hydrogen bonds) in
my protein-drug complex. I have a question about is there any influence of
the drug in my protein-drug complex.
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Re: [gmx-users] (no subject)

[Tasneem Kausar]

Number of hydrogen bond depends on the nature of your drug. It can be zero,
one or many.

On Thu, Aug 10, 2017 at 10:33 AM, saranya  wrote:

> Hi,
> I have done protein-drug simulations for 100ns. While calculating the
> hydrogen bond between the protein-drug complex I am getting only 2 hydrogen
> bonds.
> I just want to clarify that 2 hydrogen bonds mean very low, is it
> acceptable to get this minimum number of bond formation for the protein
> drug interaction?
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
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Re: [gmx-users] (no subject)

[Alex]

I think it is all pretty simple, at least from what you are describe. If
there are sufficient reason to believe that your membrane should be flat
and not jagged, and your box size (supercell size, in the terminology you
probably prefer) is properly set up, simply allow it to relax in vacuum at
a very low temperature. Say, 5-10K? This is prior to solvating, etc.
I've never worked with MnO2, so I just can't say anything more specific,
sorry.

I hope this helps.

Alex

On Wed, Aug 9, 2017 at 12:10 PM, gangotri dey  wrote:

> Dear Alex and Mark,
>
> Thank you for your kind reply.
>
> To begin with I am a Postdoc but with expertise is in DFT. It is my first
> venture into force field MD calculations. Hence, I am struggling. My group
> and the boss has similar expertise. So we have turned to public forums to
> ask questions.
>
> My system is a brick floating in the water as you have correctly
> identified.
> My system is a periodic MnO2 surface. It has triclinic crystal system. I
> want it to be solvated in all 3 directions but within the boundary of the
> unit cell. This means that I do not want any water molecule between the
> surface and its continuous periodic image. I want the water to be maximum
> in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
> insert_molecule and then -nmol and -ip option. But this still generates a
> structure with water molecules beyond the desired x and y plane. I am not
> sure how can I get this done as desired.
>
> If the question and the problem are not very clear, please let me know. I
> will try to reframe my words.
>
> Looking forward to a healthy discussion.
>
> Thank you
> G.
>
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
>
>
>
>
> On Mon, Aug 7, 2017 at 8:06 PM, Alex  wrote:
>
> >
> > I did not quite understand your comment.
> >>>
> >>> However, I am trying my best to answer it.
> >>> I have a surface MnO2 model. I have solvated the structure in all 3
> >>> directions. After that, I minimize it and run NVT simulation with the
> >>> parameters as mentioned. However, I see that there is a deformation of
> >>> the
> >>> surface and it does not remain a flat surface. Instead, it curls like a
> >>> ribbon. This should not be the case. Hence, I am wondering what are the
> >>> factors that can lead to this deformation? Are the parameters in the
> NVT
> >>> simulation good enough or else there is a problem that I cannot see.
> >>>
> >>> G
> >>>
> >>> There are a few points to be made...
> > 1. The shape of your system, which is "solvated in all 3 directions" is
> > very unclear. Is this a brick floating in water?
> > 2. Please do not solvate anything until you have established that your
> > "surface" is happy in vacuum.
> > 3. If you have bending as a whole, it could be indicative of large
> > internal strains, in which case NVT is probably a poor option. When you
> say
> > you have "a surface MnO2 model," is it something like this?
> > https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> > e-dioxide-from-xtal-sheet-3D-balls.png
> > 4. This community is mostly focused on biomolecular simulations and noone
> > will be able to verify your parameterization of a solid crystal. Here is
> > the rule of thumb though: If something bends when it shouldn't bend, your
> > model is bad, which really has nothing to do with Gromacs.
> > 5. If you are a student and points 1-4 aren't something your doctoral
> > advisor already mentioned, maybe you should find another advisor.
> >
> > Alex
> >
> >
> > Hi,
> 
>  Are you trying to implement a model that you know is capable of
> produce
>  a
>  surface that does not deform in unexpected ways?
> 
>  Mark
> 
>  On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
> 
>  Dear all,
> >
> > I am trying to equilibrate a MnO2 surface (not cluster but
> periodic). I
> > have solvated the surface with water in all 3 directions. After the
> NVT
> > run, I see that the surface is deformed. I was wondering what else
> can
> >
>  I
> >>>
>  add in my nvt.mdp to not encounter this problem?
> >
> > I have mainly followed the examples in the forum for graphene/CNT
> >
>  growth.
> >>>
>  title   = MnO2  in H2O NVT equilibration
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 5 ; 2 * 50 = 100 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 50; save coordinates every 0.10 ps
> > nstvout = 50; save velocities every 0.10 ps
> > nstenergy   = 50; save energies every 0.10 ps
> > nstlog  = 50; update log file every 0.10 ps
> 

Re: [gmx-users] (no subject)

[gangotri dey]

Dear Alex and Mark,

Thank you for your kind reply.

To begin with I am a Postdoc but with expertise is in DFT. It is my first
venture into force field MD calculations. Hence, I am struggling. My group
and the boss has similar expertise. So we have turned to public forums to
ask questions.

My system is a brick floating in the water as you have correctly
identified.
My system is a periodic MnO2 surface. It has triclinic crystal system. I
want it to be solvated in all 3 directions but within the boundary of the
unit cell. This means that I do not want any water molecule between the
surface and its continuous periodic image. I want the water to be maximum
in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
insert_molecule and then -nmol and -ip option. But this still generates a
structure with water molecules beyond the desired x and y plane. I am not
sure how can I get this done as desired.

If the question and the problem are not very clear, please let me know. I
will try to reframe my words.

Looking forward to a healthy discussion.

Thank you
G.




*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 8:06 PM, Alex  wrote:

>
> I did not quite understand your comment.
>>>
>>> However, I am trying my best to answer it.
>>> I have a surface MnO2 model. I have solvated the structure in all 3
>>> directions. After that, I minimize it and run NVT simulation with the
>>> parameters as mentioned. However, I see that there is a deformation of
>>> the
>>> surface and it does not remain a flat surface. Instead, it curls like a
>>> ribbon. This should not be the case. Hence, I am wondering what are the
>>> factors that can lead to this deformation? Are the parameters in the NVT
>>> simulation good enough or else there is a problem that I cannot see.
>>>
>>> G
>>>
>>> There are a few points to be made...
> 1. The shape of your system, which is "solvated in all 3 directions" is
> very unclear. Is this a brick floating in water?
> 2. Please do not solvate anything until you have established that your
> "surface" is happy in vacuum.
> 3. If you have bending as a whole, it could be indicative of large
> internal strains, in which case NVT is probably a poor option. When you say
> you have "a surface MnO2 model," is it something like this?
> https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> e-dioxide-from-xtal-sheet-3D-balls.png
> 4. This community is mostly focused on biomolecular simulations and noone
> will be able to verify your parameterization of a solid crystal. Here is
> the rule of thumb though: If something bends when it shouldn't bend, your
> model is bad, which really has nothing to do with Gromacs.
> 5. If you are a student and points 1-4 aren't something your doctoral
> advisor already mentioned, maybe you should find another advisor.
>
> Alex
>
>
> Hi,

 Are you trying to implement a model that you know is capable of produce
 a
 surface that does not deform in unexpected ways?

 Mark

 On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:

 Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> have solvated the surface with water in all 3 directions. After the NVT
> run, I see that the surface is deformed. I was wondering what else can
>
 I
>>>
 add in my nvt.mdp to not encounter this problem?
>
> I have mainly followed the examples in the forum for graphene/CNT
>
 growth.
>>>
 title   = MnO2  in H2O NVT equilibration
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 50 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 50; save coordinates every 0.10 ps
> nstvout = 50; save velocities every 0.10 ps
> nstenergy   = 50; save energies every 0.10 ps
> nstlog  = 50; update log file every 0.10 ps
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = none  ; 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; 20 fs, largely irrelevant
>
 with
>>>
 Verlet
> rcoulomb= 1.0   ; short-range electrostatic
>
 cutoff

> (in nm)
> rvdw  

Re: [gmx-users] (no subject)

[Justin Lemkul]

On 8/8/17 1:06 PM, Sorour Hasani wrote:

Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS.
When I run pdb2gmx, using CHARMM27 FF, I had no error.
After looking in the literature, I found their corresponding
parameters: I added the following fields in CHARMM file ffbonded.itp
[
bondtypes ]
;
i j func b0 kb
SG
FE 1 0.232 209200.0

[
angletypes ]
;
i j k func th0 cth ub0 cub
CT2
SG FE 5 100.6 418.4 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
SG
FE NPH 5 90.0 836.8 0.0 0.0
;
###
X
CS SS X 9 0.20 0.0 3
CA
CB SG FE 9 0.20 0.0 3
HB1
CB SG FE 9 0.20 0.0 3
HB1
CB SG FE 9 0.20 0.0 3
;
###
X
FE SS X 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
CB
SG FE NPH 9 0.00 0.0 4
But after that, I had another type of error:
Fatal error:
Unknown bond_atomtype SG, I correct it by default.
after that in grompp step : I got error
ERROR 7 [file topol.top, line 41571]:

No default Proper Dih. types

Fatal error:
There were 24 errors in input file(s).

what should I do?




SG is the atom *name* in cysteine, not its type.  Only atom *types* are valid in 
ffbonded.itp and ffnonbonded.itp.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] (no subject)

[Alex]

I did not quite understand your comment.

However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.

G


There are a few points to be made...
1. The shape of your system, which is "solvated in all 3 directions" is 
very unclear. Is this a brick floating in water?
2. Please do not solvate anything until you have established that your 
"surface" is happy in vacuum.
3. If you have bending as a whole, it could be indicative of large 
internal strains, in which case NVT is probably a poor option. When you 
say you have "a surface MnO2 model," is it something like this? 
https://upload.wikimedia.org/wikipedia/commons/8/81/Manganese-dioxide-from-xtal-sheet-3D-balls.png
4. This community is mostly focused on biomolecular simulations and 
noone will be able to verify your parameterization of a solid crystal. 
Here is the rule of thumb though: If something bends when it shouldn't 
bend, your model is bad, which really has nothing to do with Gromacs.
5. If you are a student and points 1-4 aren't something your doctoral 
advisor already mentioned, maybe you should find another advisor.


Alex


Hi,

Are you trying to implement a model that you know is capable of produce a
surface that does not deform in unexpected ways?

Mark

On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:


Dear all,

I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can

I

add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT

growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; 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; 20 fs, largely irrelevant

with

Verlet
rcoulomb= 1.0   ; short-range electrostatic

cutoff

(in nm)
rvdw= 1.0   ; short-range van der Waals

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 is on
tcoupl  = V-rescale ; modified Berendsen

thermostat

tc-grps = SOL MnO ; three 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 is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
periodic-molecules = yes
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
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* Please 

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

On the information given, nobody can tell whether the parameters you have
for the interactions between Mn and O and maybe water are unsuitable, or
that something is wrong with the method, or the initial conditions, or the
code.

Mark

On Mon, 7 Aug 2017 23:11 gangotri dey  wrote:

> I did not quite understand your comment.
>
> However, I am trying my best to answer it.
> I have a surface MnO2 model. I have solvated the structure in all 3
> directions. After that, I minimize it and run NVT simulation with the
> parameters as mentioned. However, I see that there is a deformation of the
> surface and it does not remain a flat surface. Instead, it curls like a
> ribbon. This should not be the case. Hence, I am wondering what are the
> factors that can lead to this deformation? Are the parameters in the NVT
> simulation good enough or else there is a problem that I cannot see.
>
> G
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
>
>
>
>
> On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Are you trying to implement a model that you know is capable of produce a
> > surface that does not deform in unexpected ways?
> >
> > Mark
> >
> > On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
> >
> > > Dear all,
> > >
> > > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> > > have solvated the surface with water in all 3 directions. After the NVT
> > > run, I see that the surface is deformed. I was wondering what else can
> I
> > > add in my nvt.mdp to not encounter this problem?
> > >
> > > I have mainly followed the examples in the forum for graphene/CNT
> growth.
> > >
> > > title   = MnO2  in H2O NVT equilibration
> > > ; Run parameters
> > > integrator  = md; leap-frog integrator
> > > nsteps  = 5 ; 2 * 50 = 100 ps
> > > dt  = 0.002 ; 2 fs
> > > ; Output control
> > > nstxout = 50; save coordinates every 0.10 ps
> > > nstvout = 50; save velocities every 0.10 ps
> > > nstenergy   = 50; save energies every 0.10 ps
> > > nstlog  = 50; update log file every 0.10 ps
> > > ; Bond parameters
> > > continuation= no; first dynamics run
> > > constraint_algorithm= lincs ; holonomic constraints
> > > constraints = none  ; 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; 20 fs, largely irrelevant
> with
> > > Verlet
> > > rcoulomb= 1.0   ; short-range electrostatic
> > cutoff
> > > (in nm)
> > > rvdw= 1.0   ; short-range van der Waals
> > 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 is on
> > > tcoupl  = V-rescale ; modified Berendsen
> > thermostat
> > > tc-grps = SOL MnO ; three 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 is off
> > > pcoupl  = no; no pressure coupling in NVT
> > > ; Periodic boundary conditions
> > > pbc = xyz   ; 3-D PBC
> > > periodic-molecules = yes
> > > ; Dispersion correction
> > > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > > ; Velocity generation
> > > gen_vel = yes   ; assign velocities from Maxwell
> > > distribution
> > > gen_temp= 300   ; temperature for Maxwell distribution
> > > gen_seed= 18; generate a random seed
> > >
> > >
> > > *Thank you*
> > >
> > > *Gangotri Dey*
> > > Postdoctoral Associate
> > > Rutgers University New Brunswick
> > > Chemistry and Chemical Biology
> > > 174 Frelinghuysen Road, Piscataway, NJ 08854
> > > Phone: +16092162254
> > > --
> > > 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
> > > 

Re: [gmx-users] (no subject)

[gangotri dey]

I did not quite understand your comment.

However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.

G



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham 
wrote:

> Hi,
>
> Are you trying to implement a model that you know is capable of produce a
> surface that does not deform in unexpected ways?
>
> Mark
>
> On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
>
> > Dear all,
> >
> > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> > have solvated the surface with water in all 3 directions. After the NVT
> > run, I see that the surface is deformed. I was wondering what else can I
> > add in my nvt.mdp to not encounter this problem?
> >
> > I have mainly followed the examples in the forum for graphene/CNT growth.
> >
> > title   = MnO2  in H2O NVT equilibration
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 5 ; 2 * 50 = 100 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 50; save coordinates every 0.10 ps
> > nstvout = 50; save velocities every 0.10 ps
> > nstenergy   = 50; save energies every 0.10 ps
> > nstlog  = 50; update log file every 0.10 ps
> > ; Bond parameters
> > continuation= no; first dynamics run
> > constraint_algorithm= lincs ; holonomic constraints
> > constraints = none  ; 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; 20 fs, largely irrelevant with
> > Verlet
> > rcoulomb= 1.0   ; short-range electrostatic
> cutoff
> > (in nm)
> > rvdw= 1.0   ; short-range van der Waals
> 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 is on
> > tcoupl  = V-rescale ; modified Berendsen
> thermostat
> > tc-grps = SOL MnO ; three 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 is off
> > pcoupl  = no; no pressure coupling in NVT
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > periodic-molecules = yes
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes   ; assign velocities from Maxwell
> > distribution
> > gen_temp= 300   ; temperature for Maxwell distribution
> > gen_seed= 18; generate a random seed
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > Postdoctoral Associate
> > Rutgers University New Brunswick
> > Chemistry and Chemical Biology
> > 174 Frelinghuysen Road, Piscataway, NJ 08854
> > Phone: +16092162254
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * 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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